| Previous changeset 0:b94ca591877b (2011-12-20) Next changeset 2:a52e6cbbb469 (2012-07-03) |
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Commit message:
Uploaded emboss functional test input and output data files. |
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added:
test-data/1.fasta test-data/2.fasta test-data/3.fasta test-data/emboss_antigenic_out.tabular test-data/emboss_backtranseq_out.fasta test-data/emboss_banana_out.txt test-data/emboss_biosed_out.fasta test-data/emboss_btwisted_out.btwisted test-data/emboss_cai_out.cai test-data/emboss_charge_out.charge test-data/emboss_chips_out.chips test-data/emboss_codcmp_out.codcmp test-data/emboss_coderet_out.coderet test-data/emboss_compseq_out.compseq test-data/emboss_cpgreport_out1.gff test-data/emboss_cpgreport_out2.cpgreport test-data/emboss_cusp_out.cusp test-data/emboss_cutseq_out.fasta test-data/emboss_dan_out.png test-data/emboss_degapseq_out.fasta test-data/emboss_descseq_out.fasta test-data/emboss_einverted_out.einverted test-data/emboss_epestfind_out.epestfind test-data/emboss_equicktandem_out.equicktandem test-data/emboss_est2genome_out.est2genome test-data/emboss_etandem_out.table test-data/emboss_extractseq_out.fasta test-data/emboss_freak_out.freak test-data/emboss_fuzznuc_out.tabular test-data/emboss_fuzzpro_out.tabular test-data/emboss_fuzztran_out.tabular test-data/emboss_garnier_out.tabular test-data/emboss_geecee_out.geecee test-data/emboss_getorf_out.fasta test-data/emboss_helixturnhelix_out.tabular test-data/emboss_hmoment_out.hmoment test-data/emboss_iep_out.iep test-data/emboss_isochore_out.isochore test-data/emboss_marscan_out.tabular test-data/emboss_maskfeat_out.fasta test-data/emboss_maskseq_out.fasta test-data/emboss_matcher_out.fasta test-data/emboss_msbar_out.fasta test-data/emboss_needle_out.score test-data/emboss_newcpgreport_out.newcpgreport test-data/emboss_newcpgseek_out.newcpgseek test-data/emboss_newseq_out.fasta test-data/emboss_noreturn_out.noreturn test-data/emboss_notseq_out.fasta test-data/emboss_nthseq_out.fasta test-data/emboss_palindrome_out.palindrome test-data/emboss_pasteseq_out.fasta test-data/emboss_patmatdb_out.tabular test-data/emboss_pepcoil_out.pepcoil test-data/emboss_pepstats_out.pepstats test-data/emboss_plotorf_out.png test-data/emboss_plotorf_out1.png test-data/emboss_polydot_out.png test-data/emboss_prettyseq_out.prettyseq test-data/emboss_primersearch.fasta test-data/emboss_primersearch_out.primersearch test-data/emboss_revseq_out.fasta test-data/emboss_seqmatchall_out.fasta test-data/emboss_seqret_out.fasta test-data/emboss_sigcleave_out.tabular test-data/emboss_sirna_out.fasta test-data/emboss_sixpack_out2.sixpack test-data/emboss_skipseq_out.fasta test-data/emboss_splitter_out.fasta test-data/emboss_supermatcher_out.fasta test-data/emboss_syco_out.syco test-data/emboss_tranalign_out.fasta test-data/emboss_transeq_out.fasta test-data/emboss_trimest_out.fasta test-data/emboss_trimseq_out.fasta test-data/emboss_union_out.fasta test-data/emboss_water_out.fasta test-data/emboss_water_out.score test-data/emboss_wobble_out.png test-data/emboss_wobble_out.wobble test-data/emboss_wordcount_out.wordcount |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.fasta Wed Mar 21 16:30:01 2012 -0400 |
| b |
| b'@@ -0,0 +1,2 @@\n+>hg17\n+gtttgccatcttttgctgctctagggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTAAAACTTCCC-------------------------------AAATACT-GCCACTGATGTCCTG-----ATGGAGGTA-------TGAA-------------------AACATCCACTAAAATTTGTGGTTTATTCATTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGGGAGATATTTGGggaaatt---ttgtatagactagctttcacgatgttagggaattattattgtgtgataatggtcttgcagttaca-cagaaattcttccttattttttgggaa---gcaccaaag----tagggat---aaaatgtcatgatgtgtgcaatacactttaaaatgtttttg-----ccaaaataatt----------------aatgaagc--aaatatggaaa-ataataattattaaatctaggtgatgggtatattgtagttcactatagtattgcacacttttctgtatgtttaaatttttcatttaaaaaaaaactttgagc-----tagacaccaggctatgagctaggagcatagcaatgaccaa----------------------------------------------------------------------------------------------atagactcctaccaa--------------------------------------------------ctc-aaagaatgcacattctCTGGGAAACATGTTTCCATTAGGAAGCCTCGAATGCAATGTGACTGTGGTCTCCAGGACCTG-TGTGATCCTGGCTTTTCCTGTTCCCTCCG---CATCATCACTGCAGGTGTGTTTTCCCAAGTTTTAAACATTTA------CCTTCCCAGTGGCCTTGCGTCTAGAGGAATCCCTGTATAGTGGT-ACATGAATATAACACATAACAAA-AATCATCTCTATGGTGTGTGTTGTTCCTGGGGTTCAattcagcaaattttccctg-ggcacccatgtgttcttggcactggaaaagtaccgggactgaaacagttgatggccca-atccctgtcctct---taaaacctaagggaggagaTGGAAAGGGG-CACCCAACCCAGACTGAGAGACAGGAATTAGCTGCAAGGGGAACTAGGAAAAGCTTCTTTA---AGGATGGAGAGGCCCTAGTGGAAT-GGGGAGATTCTTCCGGGAGAAGCGATGGATGCACAGTTGGGCATCCCCACAGACGGACTGGAAAGAAAAAAGGCCTGGAGGAATCAATGTG-------CAATGTATGTGTGTTCCCTGGTTcaagggctgg-gaactttctcta-aagggccaggtagaaaacattttaggctttctaagccaag--gcaaaat-tgaggatattacatgggtacttatacaacaagaataaacaatt---tacacaattttttgttgacagaattcaaaactttat----agacacagaaatgcaaatttcctgtaattttcccat-gagaactattcttct--tttgttttgttttgcgacAGGGTTGCGCtgatcctcccgcctcagtctccctaagtgctgagatgttgcaggaagtcagggaccccgaacagagagatcggctggagccgtggcagaggaacataaattttgaagatttcattttaatatggacacttatcagttcccaaataatacttttataattttttatgcctgtctttgctttaatctcttaatcctgttatcttcataagctaaggatgtacgtcacctcaggaccactgtgataattgtgttaactgtacagattgattgcaaaacatgtgtgtttgaacaatatgaaatcagtgcaccttgaaaaagagcagaataacagcaatttttagggaacaagggaagacaactataaggtctgactgcctgcggggtcgggcaaagggagccatatttttcttcttgcagagagcctataaatagacctgcaagtaggagagatattgctaatttcttttgctagcatggaatattaatattaacaccctgggaaaggaatgcattcctggggggaggtctataaatggccgctctgggaatgtctatcctacgcaatggagataaggactgagatacgccctggtctcctgcagtaccctcaggcttactagggtggtgaaaaactccgccctggtaaatttgtggtcagaccagttttctgctctcgaacactgttttctgttgtttaagatgtttatcaagacaatacgtgcaccgctgaacacagacccttatcagtagttctcctttttgccctttgaagcatgtgatctactccctgttttacaccccctcaccttttgaaacccttaataaaaaacttgctggttt-gaggctcaggtgggcatcacagtactaccgatatgtgatgtcacccccggcggcccagctgtaaaattcctctctttgtactctctctctttatttctcagccagctgacacttatggaaaatagaaagaacctacgttgaaatattgggggcaggttcccccaataTCTGGTGCCCAACGTGGGAtactgagattacaagcatgagccactgcatctggcctcttcttttgatttttttttttcaaacttttacaaatgtagaaaccattcttagcttttgggcattaccaaacccggcagtgg-caggctcggttcaccaacgtcatttgcagttccccgCTTTATGTTATGGgttttgttttgttttgtttttttt-attgagacagagtttcactcttgttgcccaggctgtagtgcaatggtctgatcttggctcactgcaacctccacttcccaggttcaagccattctcctgcctcagcctctcaagtagctgggattacagacactcaccaccacacctggctaattttgtatttttagtagagatgaggtttcaccatgttggccaggctggtctcgaaatcctgacctcaggtgatccacccaccttggcctcccaaagtgctgggattacaggcttgagctaccacgcctggctGGGTTGGTTCTCAATGGAGTGGTTTGTTTTTGGAGCTGCTCT-GCGCAGtggggaccagaataggcctg-------------------ggttcctagcccattgctattcctt----accagctgtggattctaaggaaagtcatttaacctcgctggaccttag-attcctcatccctgaaGCCCAAGGGTaaaacaaaacaaaacaaaacaaaacaaaccaaCCCATCATGTAAAGCGGGGAACTACAAACGATACAGGTGAAACATGCCTACCACACCACTCACAGGCT--ATGATGACAAAAACGTGGCTACATCTGGGACCACCCCCCAACCCCCACTTTGTACGTAGGAAATACGGAGTTGAGGATGGAGACCCACAGTATGTCCAGAGTGTCCCCAAAGGCCACAGTGCCCGCCTGGAGCCCTCCAGAGAGCGTGCACTCCCTGGGGTGCCAGCCAGAGACAACTTGCCCTGAGGCTTGGAACTCGATTCTCCGCGTGCCAGAGAAGGGGTGGGACTTCAGAACCCCCAACCCCGCAATCTGGGTCGGGGAGCCTGGCGCACTGCGGGCCGCTCCCTCTAACCCTGGGCTTCCCTG------GCGTCCAGGGCCGTCGG------'..b'gataatggggatatcacacacta-ttcacaaggttgttatgaggcctaaattagctaaagcaATTGAATCCTCCTTACCCCCTGCATGGAGCTCTCTGGAGACTTCCACGTCTCCTGGTCATTGTGGGTGTCTTATGGTA-GTCTTGGGCAGTTAGGGAGAAGTTAGGTGTCTGGAAGCAAAGATGGCTCAGAACTAGATAGAGTC-TTGGGCATTTTATA-GATAAAAACTCTT--GTCTCCtttaaaaataataaaaaaaaattaGCTGGGCATATTAGCCACTCAGCAAGACTGCACGTGATAGATCCCGAGTGCCCCACCTTGGGTGGTGTAATACACAATATCACGGGAGCCCCGGGTAGTAACCACGGAGGTGTCAGCCTCAGTGCTGTGGGCAGATG-GATGGGGAGAGCC--TCCCGG-AACTGGAGTCACTGGAGCA----------------------------GGGTTGGGGGGCCTCACTGAGGGTACGGCCTTGATCTCTAAGGAGGAGGGACTGCCTGGAAAAGC-TGACTGGGAGGGAGGACTCGGCTGGGGGTAGAAGGGA----------CTAGGGAAGGCTGGGGGTGGGGGTGCTTATGGAGGACCTCAGATGCCTGGGGAACAGACTCCACTAAATAAAACATATGAAACCATGGCTGGTTCTTCAGCAGAGGCCATGTAGAGAAAGGAATGACCTAGGAAAGTTGGCCTGGAAGTGGAGGGAAGGATGGTGTGGGAAAAGCAGGAA--------TCTCGGAGACCAGCTTAGAGGCTTGGCAGTCACCTGGGTGCAGG-ATACAAGGGCCTGAGCCAAAGTGGTGAGGGAGGGTGGAAGGAGGCAGCCCAGAGAATGACCCTCCATGCCCACGGGGAAGGCAGAGGGCTCT-GAGAGCGA--TTCCTCCCACATG-CT-GAGCACTTGTTCTCCCTCTTCCTCCTGCATAGCAGTCAGTCTCCTCCAAACAGAAAGTCACCGGTTTGGACTTCATTCCTGGGCTCCACCCCATCCTGACCTTATCCAAGATGGACCAGACACTGGCAGTCTACCAACAGATCCTCACCAGTATGCCTTCCAGAAACGTGATCCAAATATCCAACGACCTGGAGAACCTCCGGGATCTTCTTCACGTGCTGGCCTTCTCTAAGAGCTGCCACTTGCCCTGGGCCAGTGGCCTGGAGACCTTGGACAGCCTGGGGGGTGTCCTGGAAGCTTCAGGCTACTCCACAGAGGTGGTGGCCCTGAGCAGGCTGCAGGGGTCTCTGCAGGACATGCTGTGGCAGCTGGACCTCAGCCCTGGGTGCTGAGGCCTTGAAGGTCACTCTTCCTGCAAGGACTACGTTAAGGGAAGGAACTCTGGCTTCCAGGTATCTCCAGGATTGAAGAGCATTGCATGGACACCCCTTATCCAGGACTCTGTCAATT--TCCCTGACTCCTCTAAGCCACTCTTCCAAAGGCATAAGACCCTAAGCCTCCTTTTGCTTGAAACCAAAGATATATACACAGGATCCTATTCTCACCAGGAAGGGGG-TCCACCC-AGCAAAGAGTGGGCTGCATCTGGGATTCCCACCAAGGTCTTCAGCCATCA---ACAAGAGTTGTCTTGTCCCCTCT-TGACCCATCT-----------------CCCCCTCACTGAATGCCTCAATGTGACCAGGGGTGATTTCAGAGAGGGCAGAGGGGTAGGCAGAGCCTTTGGATGACCA--GAACAAGGTTCCCTCTGAGAATTCCAAGGAGTTCCATGAAGACCACATCCACACACG--CAGGAACTCCC--AGCAACACAAGCTGGAA---GCACATGTTTATTTATTCTGCATTTTATTCTGGATGGATTTGAAGCAAAGCACCAGCTTCTCCAGGCTCTTTGGGGTCAGCCAGGGCCAGGGGTCTCCCTGGAGTGCAGTTTCCAATCCCATAGATGGGTC-TGGCTGAGCTGAACCCA---TTTTGAGTGACT----CGAGGGTTGGG-TTCATCTGAGCAAGAGCTGGCAAAGGTGGCTCTCCAGTTAGTTCTCTCGTAACTGGTTTCATTTCTACTGTGACTGATGTTACATCACAGTGTTTGCAATGGTGTTGCCCTGAGTGGATCTCCAAGGACCAGGTTATTTTAAAA---AGATTTGTTTTGTCAAGTGTCATATGTAGGTGTCTGCACCCAGGGGTGGG-GAATGTTTGGGCAGAAGGGAGAAGGATCTAGAATGTGTTTTCTGAATAACATTTGTGTGGTGGGTTCTTTGGAAGGAGTGAGA-TCATTTTCTTATCTTCTGCAATTGCTTAGGATGTTTTTCATGAAAA------------TAGCTCTTTCAG-GGGGGTTGTGAGGCCTGGCCAGGCACCCCCTGGAGAGAAGTTTCTGGCCCTGGCTGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAAAGGGCTGAAAGCCATTTGTTGGGGCAGTGGTAAGCTCTGGCTTTCTCCGACTGCTAGGGAGTGGTCTTTCCTATCATGGAGTGACGGTCCCACACTGGTGACTGCGATCTTCAGAGCAGGGGTCCTTGGTGT-GACCCTCTGAATGGTCCAGGGTTGATCACACTCTGGGTTTATTACATGGCAG-----TGTTCCTATTTGGGGCTTGCATGCCAAATTGTAGTTCTTGTCTGATTGGCTCACCC-AAGCAAGGCCAAAATTACCAAAAATCTTGGGGGG--TTTTTACTC-CAGTGGTGAAGAAAACTCCTTTAGCAGG-TGGTCCTGAGACCT-GACAAGCACTGCTAGGCGAGTGCCAGGACTCCCCAGGCCAGGCCACCAGGATGGCCCTTCCCACTGGAGGTCACATTCAGGAAGATGAAAGAGGAGGTTTGGGGTCTGCCACCATCCTGCTGCTGTGTTTTTGCTATCACACAGTGGGTGGTGGATCTGTCCAAGGAAACTTGAATCAAAGCAGTTAAC-TTTAAGactgagcacctgcttcatgctcagccctgactggtgctataggctggagaagctcacccaataaacattaagatt-gaggcctgccctcagggatcttgcattcccagtggTCAAACC-GCACTCACCCATGTGCCAAGGTGGGGTA-TTTACCACAGCAG--CTGAACAGCCAAATGCATGGTGCAGTTGACAGCAGGTGGGAAATGGTATGAGCTGAGGGGGGCCGTGCCCAGGGGCCCACAGG-GAACCCTGCTTGCACTTTGTAACATGTTTA-----CTTTTCagggcatcttagctt---ctatta-----tagccacatccctttga---aacaagataactgagaatttaaaaataagaa-----aata--TGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAAATGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCATGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCA\n' |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2.fasta Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,11 @@ +>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +gttcgatgcc taaaatacct tcttttgtcc ctacacagac cacagttttc ctaatggctt +tacaccgact agaaattctt gtgcaagcac taattgaaag cggttggcct agagtgttac +cggtttgtat agctgagcgc gtctcttgcc ctgatcaaag gttcattttc tctactttgg +aagacgttgt ggaagaatac aacaagtacg agtctctccc ccctggtttg ctgattactg +gatacagttg taataccctt cgcaacaccg cgtaactatc tatatgaatt attttccctt +tattatatgt agtaggttcg tctttaatct tcctttagca agtcttttac tgttttcgac +ctcaatgttc atgttcttag gttgttttgg ataatatgcg gtcagtttaa tcttcgttgt +ttcttcttaa aatatttatt catggtttaa tttttggttt gtacttgttc aggggccagt +tcattattta ctctgtttgt atacagcagt tcttttattt ttagtatgat tttaatttaa +aacaattcta atggtcaaaa a \ No newline at end of file |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/3.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3.fasta Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,50 @@ +>HSFAU1 +ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc +agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg +cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc +tcctggcaggccccctggaggatgaggccactctgggccagtgcggggtggaggccc +tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc +gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga +agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca +cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc +tctaataaaaaagccacttagttcagtcaaaaaaaaaa +>HSFAU2 +ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc +agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg +cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc +tcctggcaggcgcgcccctggaggatgcactctgggccagtgcggggtggaggccc +tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc +gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga +agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca +cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc +tctaataaaaaagccacttagttcagtcaaaaaaaaaa +>HSFAU3 +ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc +agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg +cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc +tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc +tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc +gtgctggaaaagtgagaggtcagactcctaagggggccaaacaggagaagaagaagaaga +agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca +cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc +tctaataaaaaagccacttagttcagtcaaaaaaaaaa +>HSFAU4 +ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc +agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg +cccagatcaaggctcatgaaatagcctcactggagggcattgccccggaagatcaagtcgtgc +tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc +tgactaccctggaagtagcaggccgcatgcttgcccgaggtaaagttcatggttccctggccc +gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga +agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca +cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc +tctaataaaaaagccacttagttcagtcaaaaaaaaaa +>HSFAU5 +ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc +agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg +cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc +tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc +tgactaccctggaagtaggccgcatgctttttggaggtaaagttcatggttccctggccc +gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga +agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca +cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc +tctaataaaaaagccacttagttcagtcaaaaaaaaaa \ No newline at end of file |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_antigenic_out.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_antigenic_out.tabular Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,23 @@ +SeqName Start End Score Strand Max_score_pos +Sequence 196 225 1.340 + 221 +Sequence 253 283 1.263 + 266 +Sequence 27 45 1.241 + 32 +Sequence 60 72 1.236 + 66 +Sequence 357 368 1.214 + 360 +Sequence 130 159 1.191 + 148 +Sequence 83 93 1.186 + 87 +Sequence 165 175 1.147 + 173 +Sequence 6 22 1.147 + 20 +Sequence 293 301 1.147 + 299 +Sequence 324 343 1.147 + 330 +Sequence 473 481 1.142 + 479 +Sequence 540 551 1.119 + 545 +Sequence 501 510 1.114 + 504 +Sequence 409 415 1.097 + 412 +Sequence 48 56 1.097 + 51 +Sequence 553 558 1.092 + 558 +Sequence 106 112 1.087 + 110 +Sequence 488 494 1.075 + 490 +Sequence 423 429 1.075 + 426 +Sequence 118 123 1.070 + 118 +Sequence 239 247 1.042 + 245 |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_backtranseq_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_backtranseq_out.fasta Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,30 @@ +>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +GGCACCACCTGCGGCGCCACCGGCTGCTGCACCGCCGCCGCCGCCACCGCCTGCTGCACC +ACCTGCACCACCACCACCGGCACCTGCTGCTGCACCGCCTGCGCCTGCGCCGGCGCCTGC +TGCGCCTGCGCCGGCACCACCACCACCTGCTGCACCGCCGCCACCGGCGGCTGCACCACC +ACCGCCTGCGCCTGCTGCGGCGCCTGCACCGCCGGCGCCGCCGCCACCACCTGCACCACC +GGCACCGGCTGCGCCGCCGGCTGCGCCTGCACCGCCGCCACCACCGGCGCCGCCGCCGGC +TGCGGCGGCACCACCGGCGGCTGCTGCACCGCCGGCGCCGGCACCGGCACCACCGCCTGC +TGCGGCGGCACCACCACCGGCACCGCCACCGCCGGCTGCACCGGCGCCGGCTGCGGCTGC +GGCACCTGCACCTGCACCACCGGCTGCTGCTGCACCGGCGCCACCTGCGCCGCCGCCGGC +GGCACCACCTGCGCCACCACCACCACCTGCACCTGCACCGCCTGCACCACCACCGGCGGC +GCCGCCGGCGCCTGCGGCACCACCGGCACCGGCGGCGCCGCCGGCGCCGCCACCGCCTGC +GCCGCCTGCGCCGCCGGCACCGCCTGCGGCGCCGGCACCTGCACCTGCACCTGCTGCTGC +TGCTGCTGCACCGGCGGCACCACCACCGGCTGCACCGGCGCCACCACCGCCTGCACCGGC +GGCGCCACCGCCTGCGCCGGCACCACCGGCACCGCCGCCACCGCCTGCTGCTGCACCACC +TGCGGCTGCGCCGCCTGCGCCTGCTGCGGCTGCGGCACCGCCGCCTGCACCGCCACCTGC +ACCGCCACCGCCACCGGCGCCGCCACCACCGCCACCACCACCACCTGCTGCTGCACCACC +ACCGCCACCACCGCCACCGCCACCGGCACCGCCGGCACCGCCGGCGGCACCACCTGCGGC +ACCTGCACCACCACCGCCGCCACCTGCACCACCTGCTGCACCACCACCGCCGGCTGCGCC +GCCGGCACCTGCACCACCACCACCGCCTGCACCGGCACCACCACCACCTGCGGCGCCTGC +TGCACCTGCGCCGCCACCGGCACCACCTGCGCCACCGGCACCACCTGCACCACCGCCGGC +GGCACCACCGGCACCACCACCACCGGCGGCGCCACCGCCGCCACCGCCACCGGCTGCGGC +GGCACCTGCGCCGGCACCACCACCGCCGCCACCTGCACCACCTGCGGCACCACCGGCACC +ACCACCTGCACCACCTGCACCACCGCCGCCGCCGCCACCGCCACCACCACCGCCACCACC +TGCGCCACCGGCGGCACCACCACCGCCGCCACCACCACCACCACCGGCGGCACCACCACC +GGCACCGCCTGCACCACCGGCACCACCTGCGCCGGCGGCGGCGGCTGCTGCGCCGGCACC +ACCTGCGCCACCACCGCCACCACCACCGCCTGCACCTGCACCGGCACCACCACCGGCACC +GCCACCGCCTGCGCCGGCTGCGCCGGCACCACCTGCACCACCACCACCGCCACCACCACC +ACCACCGCCGGCACCGCCACCGGCGCCACCACCACCACCGCCGCCACCACCACCGCCGCC +GCCGCCTGCGCCGCCACCACCTGCACCGCCGCCACCGGCGGCACCTGCGCCGCCGCCGCC +GCC |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_banana_out.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_banana_out.txt Wed Mar 21 16:30:01 2012 -0400 |
| b |
| b'@@ -0,0 +1,562 @@\n+Base Bend Curve\n+g 0.0 0.0\n+t 10.8 0.0\n+t 18.5 0.0\n+c 26.9 0.0\n+g 22.1 0.0\n+a 19.5 0.0\n+t 20.7 0.0\n+g 26.2 0.0\n+c 25.2 0.0\n+c 12.5 0.0\n+t 6.8 0.0\n+a 3.4 0.0\n+a 0.0 0.0\n+a 1.3 0.0\n+a 5.9 0.0\n+t 10.6 0.0\n+a 14.9 0.0\n+c 17.7 0.0\n+c 17.3 0.0\n+t 13.3 0.0\n+t 10.2 23.2\n+c 13.9 22.5\n+t 8.8 21.7\n+t 0.0 20.6\n+t 5.7 19.2\n+t 13.9 17.7\n+g 17.3 16.5\n+t 15.1 15.5\n+c 16.1 14.7\n+c 18.7 13.9\n+c 12.5 13.2\n+t 9.7 12.5\n+a 14.5 11.8\n+c 19.1 11.1\n+a 19.1 10.6\n+c 15.3 10.0\n+a 12.2 9.2\n+g 14.3 7.9\n+a 17.7 6.4\n+c 17.7 5.0\n+c 19.5 3.5\n+a 19.1 2.9\n+c 15.3 3.9\n+a 16.3 5.5\n+g 15.5 6.8\n+t 6.3 7.8\n+t 0.0 8.5\n+t 5.0 9.3\n+t 11.0 10.0\n+c 15.1 10.8\n+c 12.5 11.6\n+t 6.8 12.5\n+a 4.5 13.4\n+a 12.4 14.3\n+t 19.7 15.1\n+g 25.2 15.7\n+g 28.5 16.2\n+c 20.7 16.6\n+t 8.8 17.0\n+t 3.4 17.5\n+t 9.3 18.1\n+a 14.5 18.5\n+c 19.1 18.6\n+a 19.5 18.5\n+c 16.5 18.3\n+c 21.1 18.0\n+g 22.3 17.4\n+a 18.3 16.3\n+c 13.2 15.1\n+t 7.2 13.8\n+a 9.0 12.6\n+g 10.2 11.4\n+a 5.0 10.9\n+a 1.3 11.0\n+a 2.4 11.4\n+t 6.1 11.9\n+t 10.2 12.3\n+c 13.9 12.5\n+t 13.9 12.4\n+t 13.9 12.4\n+g 19.1 12.6\n+t 20.5 12.9\n+g 19.7 13.2\n+c 15.3 13.1\n+a 13.9 12.7\n+a 20.7 12.2\n+g 22.1 11.8\n+c 20.5 11.5\n+a 20.1 11.3\n+c 13.2 10.9\n+t 6.8 10.2\n+a 4.5 9.6\n+a 2.4 9.9\n+t 6.7 10.9\n+t 14.3 12.1\n+g 13.7 13.2\n+a 5.0 13.8\n+a 8.8 13.6\n+a 20.7 12.9\n+g 24.5 12.1\n+c 19.9 11.3\n+g 16.5 10.3\n+g 14.9 9.0\n+t 11.4 7.5\n+t 14.3 6.2\n+g 25.2 5.2\n+g 32.5 4.4\n+c 25.2 4.0\n+c 12.5 3.8\n+t 7.2 3.4\n+a 9.0 2.8\n+g 14.3 2.4\n+a 18.3 2.5\n+g 20.1 2.8\n+t 19.1 3.1\n+g 14.5 3.2\n+t 9.3 3.1\n+t 9.3 2.6\n+a 14.9 2.5\n+c 16.5 2.7\n+c 15.3 2.7\n+g 16.5 2.6\n+g 14.9 2.8\n+t 6.3 2.9\n+t 5.7 2.8\n+t 13.9 2.3\n+g 14.5 1.6\n+t 10.6 0.6\n+a 9.2 0.7\n+t 8.2 1.8\n+a 16.1 2.7\n+g 24.5 3.7\n+c 19.1 4.6\n+t 15.7 5.6\n+g 17.7 6.4\n+a 21.1 7.1\n+g 24.5 7.7\n+c 24.5 8.1\n+g 24.5 8.2\n+c 21.1 8.0\n+g 17.7 7.8\n+t 14.3 7.7\n+c 14.3 7.7\n+t 14.3 7.9\n+c 13.9 8.4\n+t 13.9 9.1\n+t 15.3 10.2\n+g 26.2 11.3\n+c 26.2 12.2\n+c 18.7 12.7\n+c 15.7 12.9\n+t 15.7 12.9\n+g 17.5 12.9\n+a 17.3 13.0\n+t 17.5 13.2\n+c 14.3 13.3\n+a 5.7 13.3\n+a 8.8 13.2\n+a 17.3 13.0\n+g 17.7 12.9\n+g 14.9 12.7\n+t 10.8 12.6\n+t 13.7 12.6\n+c 19.7 12.6\n+a 12.4 12.7\n+t 1.3 12.9\n+t 0.0 13.1\n+t 5.0 13.1\n+t 10.2 12.9\n+c 14.3 12.6\n+t 14.3 12.3\n+c 9.0 11.9\n+t 9.7 11.6\n+a 15.5 11.2\n+c 17.9 10.6\n+t 8.8 9.9\n+t 5.7 9.0\n+t 14.3 8.1\n+g 15.1 7.4\n+g 11.0 6'..b' 17.7 11.7\n+g 14.9 11.2\n+t 11.4 10.6\n+t 13.9 10.3\n+g 14.5 10.2\n+t 6.3 10.2\n+t 0.0 10.2\n+t 5.7 10.4\n+t 14.3 11.0\n+g 15.1 11.5\n+g 14.9 11.9\n+a 13.3 12.0\n+t 7.8 12.0\n+a 4.5 12.0\n+a 5.9 12.0\n+t 9.2 12.1\n+a 15.6 12.2\n+t 20.7 11.8\n+g 22.1 11.3\n+c 19.9 10.5\n+g 16.5 9.8\n+g 17.7 8.9\n+t 17.7 7.9\n+c 15.7 6.9\n+a 16.3 5.8\n+g 15.5 5.0\n+t 6.3 4.5\n+t 3.4 4.5\n+t 6.4 5.1\n+a 4.5 6.2\n+a 10.1 7.8\n+t 14.1 9.7\n+c 13.9 11.7\n+t 13.3 13.4\n+t 18.5 14.9\n+c 22.3 15.9\n+g 14.9 16.5\n+t 11.4 16.9\n+t 13.9 17.0\n+g 14.5 16.8\n+t 6.3 16.2\n+t 5.0 15.3\n+t 10.2 14.0\n+c 13.9 12.6\n+t 13.3 11.1\n+t 10.2 9.7\n+c 13.9 8.5\n+t 11.7 7.2\n+t 6.4 6.1\n+a 3.4 5.5\n+a 0.0 5.7\n+a 1.3 6.7\n+a 5.9 7.9\n+t 9.2 9.1\n+a 5.9 9.8\n+t 1.3 10.1\n+t 3.4 10.3\n+t 7.8 10.7\n+a 5.9 11.0\n+t 6.1 11.3\n+t 13.7 11.4\n+c 19.7 11.2\n+a 21.7 10.8\n+t 19.7 10.4\n+g 17.7 10.4\n+g 14.9 10.8\n+t 6.3 11.3\n+t 3.4 11.8\n+t 6.4 12.2\n+a 4.5 12.6\n+a 2.4 12.9\n+t 1.3 13.2\n+t 0.0 13.3\n+t 0.0 13.2\n+t 5.7 12.8\n+t 14.3 12.3\n+g 17.7 12.1\n+g 14.9 12.0\n+t 6.3 12.0\n+t 5.7 12.1\n+t 13.9 12.2\n+g 14.5 12.3\n+t 12.0 12.4\n+a 15.5 12.5\n+c 17.9 12.9\n+t 13.9 13.2\n+t 13.9 12.8\n+g 14.5 11.9\n+t 10.8 10.9\n+t 13.7 10.1\n+c 15.7 9.7\n+a 15.7 9.7\n+g 18.7 9.8\n+g 19.7 9.7\n+g 26.2 9.2\n+g 32.5 8.8\n+c 25.2 8.6\n+c 15.7 8.5\n+a 16.3 8.4\n+g 15.5 8.4\n+t 10.8 8.4\n+t 13.7 8.6\n+c 19.7 8.8\n+a 12.4 8.7\n+t 4.5 8.5\n+t 7.8 8.1\n+a 5.9 7.9\n+t 1.3 7.8\n+t 3.4 7.8\n+t 9.3 7.9\n+a 15.5 8.2\n+c 18.3 8.5\n+t 14.3 8.8\n+c 12.2 9.1\n+t 15.3 9.2\n+g 14.5 9.0\n+t 6.3 8.4\n+t 5.7 7.5\n+t 13.9 6.4\n+g 14.5 5.5\n+t 10.6 4.9\n+a 9.2 4.5\n+t 10.6 4.1\n+a 14.5 3.8\n+c 15.3 3.7\n+a 19.1 3.8\n+g 22.1 3.9\n+c 16.7 4.2\n+a 16.3 4.8\n+g 15.5 5.6\n+t 10.8 6.6\n+t 10.2 7.6\n+c 13.9 8.6\n+t 8.8 9.7\n+t 0.0 10.8\n+t 3.4 11.8\n+t 7.8 12.6\n+a 5.9 12.8\n+t 1.3 12.4\n+t 0.0 11.8\n+t 0.0 11.2\n+t 3.4 10.6\n+t 6.8 9.8\n+a 13.2 9.0\n+g 15.5 8.2\n+t 10.6 7.8\n+a 15.6 7.8\n+t 19.7 8.2\n+g 17.5 8.8\n+a 10.1 9.2\n+t 1.3 9.3\n+t 0.0 9.0\n+t 3.4 8.5\n+t 6.4 7.9\n+a 4.5 7.1\n+a 2.4 6.1\n+t 1.3 5.0\n+t 3.4 3.8\n+t 6.4 2.6\n+a 3.4 2.4\n+a 0.0 90.8\n+a 6.3 0.0\n+a 14.5 0.0\n+c 13.9 0.0\n+a 6.7 0.0\n+a 2.4 0.0\n+t 6.1 0.0\n+t 10.2 0.0\n+c 9.0 0.0\n+t 6.8 0.0\n+a 4.5 0.0\n+a 12.4 0.0\n+t 19.7 0.0\n+g 17.7 0.0\n+g 17.7 0.0\n+t 17.7 0.0\n+c 14.3 0.0\n+a 5.7 0.0\n+a 0.0 0.0\n+a 0.0 0.0\n+a 0.0 0.0\n+a 0.0 0.0\n' |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_biosed_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_biosed_out.fasta Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,11 @@ +>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +GTTCGAGTCCTAAAATACCTTCTTTTGTCCCTACACAGACCACAGTTTTCCTAAGTGCTT +TACACCGACTAGAAATTCTTGTGCAAGCACTAATTGAAAGCGGTTGGCCTAGAGTGTTAC +CGGTTTGTATAGCTGAGCGCGTCTCTTGCCCTGATCAAAGGTTCATTTTCTCTACTTTGG +AAGACGTTGTGGAAGAATACAACAAGTACGAGTCTCTCCCCCCTGGTTTGCTGATTACTG +GATACAGTTGTAATACCCTTCGCAACACCGCGTAACTATCTATAGTAATTATTTTCCCTT +TATTATAGTTAGTAGGTTCGTCTTTAATCTTCCTTTAGCAAGTCTTTTACTGTTTTCGAC +CTCAAGTTTCAGTTTCTTAGGTTGTTTTGGATAATAGTCGGTCAGTTTAATCTTCGTTGT +TTCTTCTTAAAATATTTATTCAGTGTTTAATTTTTGGTTTGTACTTGTTCAGGGGCCAGT +TCATTATTTACTCTGTTTGTATACAGCAGTTCTTTTATTTTTAGTAGTATTTTAATTTAA +AACAATTCTAAGTGTCAAAAA |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_btwisted_out.btwisted --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_btwisted_out.btwisted Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,7 @@ +# Output from BTWISTED +# Twisting calculated from 1 to 561 of Sequence +Total twist (degrees): 19085.5 +Total turns : 53.02 +Average bases per turn: 10.58 +Total stacking energy : -4107.68 +Average stacking energy per dinucleotide: -7.34 |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_cai_out.cai --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_cai_out.cai Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,1 @@ +Sequence: Sequence CAI: 0.188 \ No newline at end of file |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_charge_out.charge --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_charge_out.charge Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,560 @@ +CHARGE of Sequence from 1 to 561: window 5 + +Position Residue Charge +1 G 0.000 +2 T 0.000 +3 T 0.000 +4 C 0.000 +5 G 0.000 +6 A 0.000 +7 T 0.000 +8 G 0.000 +9 C 0.000 +10 C 0.000 +11 T 0.000 +12 A 0.000 +13 A 0.000 +14 A 0.000 +15 A 0.000 +16 T 0.000 +17 A 0.000 +18 C 0.000 +19 C 0.000 +20 T 0.000 +21 T 0.000 +22 C 0.000 +23 T 0.000 +24 T 0.000 +25 T 0.000 +26 T 0.000 +27 G 0.000 +28 T 0.000 +29 C 0.000 +30 C 0.000 +31 C 0.000 +32 T 0.000 +33 A 0.000 +34 C 0.000 +35 A 0.000 +36 C 0.000 +37 A 0.000 +38 G 0.000 +39 A 0.000 +40 C 0.000 +41 C 0.000 +42 A 0.000 +43 C 0.000 +44 A 0.000 +45 G 0.000 +46 T 0.000 +47 T 0.000 +48 T 0.000 +49 T 0.000 +50 C 0.000 +51 C 0.000 +52 T 0.000 +53 A 0.000 +54 A 0.000 +55 T 0.000 +56 G 0.000 +57 G 0.000 +58 C 0.000 +59 T 0.000 +60 T 0.000 +61 T 0.000 +62 A 0.000 +63 C 0.000 +64 A 0.000 +65 C 0.000 +66 C 0.000 +67 G 0.000 +68 A 0.000 +69 C 0.000 +70 T 0.000 +71 A 0.000 +72 G 0.000 +73 A 0.000 +74 A 0.000 +75 A 0.000 +76 T 0.000 +77 T 0.000 +78 C 0.000 +79 T 0.000 +80 T 0.000 +81 G 0.000 +82 T 0.000 +83 G 0.000 +84 C 0.000 +85 A 0.000 +86 A 0.000 +87 G 0.000 +88 C 0.000 +89 A 0.000 +90 C 0.000 +91 T 0.000 +92 A 0.000 +93 A 0.000 +94 T 0.000 +95 T 0.000 +96 G 0.000 +97 A 0.000 +98 A 0.000 +99 A 0.000 +100 G 0.000 +101 C 0.000 +102 G 0.000 +103 G 0.000 +104 T 0.000 +105 T 0.000 +106 G 0.000 +107 G 0.000 +108 C 0.000 +109 C 0.000 +110 T 0.000 +111 A 0.000 +112 G 0.000 +113 A 0.000 +114 G 0.000 +115 T 0.000 +116 G 0.000 +117 T 0.000 +118 T 0.000 +119 A 0.000 +120 C 0.000 +121 C 0.000 +122 G 0.000 +123 G 0.000 +124 T 0.000 +125 T 0.000 +126 T 0.000 +127 G 0.000 +128 T 0.000 +129 A 0.000 +130 T 0.000 +131 A 0.000 +132 G 0.000 +133 C 0.000 +134 T 0.000 +135 G 0.000 +136 A 0.000 +137 G 0.000 +138 C 0.000 +139 G 0.000 +140 C 0.000 +141 G 0.000 +142 T 0.000 +143 C 0.000 +144 T 0.000 +145 C 0.000 +146 T 0.000 +147 T 0.000 +148 G 0.000 +149 C 0.000 +150 C 0.000 +151 C 0.000 +152 T 0.000 +153 G 0.000 +154 A 0.000 +155 T 0.000 +156 C 0.000 +157 A 0.000 +158 A 0.000 +159 A 0.000 +160 G 0.000 +161 G 0.000 +162 T 0.000 +163 T 0.000 +164 C 0.000 +165 A 0.000 +166 T 0.000 +167 T 0.000 +168 T 0.000 +169 T 0.000 +170 C 0.000 +171 T 0.000 +172 C 0.000 +173 T 0.000 +174 A 0.000 +175 C 0.000 +176 T 0.000 +177 T 0.000 +178 T 0.000 +179 G 0.000 +180 G 0.000 +181 A 0.000 +182 A 0.000 +183 G 0.000 +184 A 0.000 +185 C 0.000 +186 G 0.000 +187 T 0.000 +188 T 0.000 +189 G 0.000 +190 T 0.000 +191 G 0.000 +192 G 0.000 +193 A 0.000 +194 A 0.000 +195 G 0.000 +196 A 0.000 +197 A 0.000 +198 T 0.000 +199 A 0.000 +200 C 0.000 +201 A 0.000 +202 A 0.000 +203 C 0.000 +204 A 0.000 +205 A 0.000 +206 G 0.000 +207 T 0.000 +208 A 0.000 +209 C 0.000 +210 G 0.000 +211 A 0.000 +212 G 0.000 +213 T 0.000 +214 C 0.000 +215 T 0.000 +216 C 0.000 +217 T 0.000 +218 C 0.000 +219 C 0.000 +220 C 0.000 +221 C 0.000 +222 C 0.000 +223 C 0.000 +224 T 0.000 +225 G 0.000 +226 G 0.000 +227 T 0.000 +228 T 0.000 +229 T 0.000 +230 G 0.000 +231 C 0.000 +232 T 0.000 +233 G 0.000 +234 A 0.000 +235 T 0.000 +236 T 0.000 +237 A 0.000 +238 C 0.000 +239 T 0.000 +240 G 0.000 +241 G 0.000 +242 A 0.000 +243 T 0.000 +244 A 0.000 +245 C 0.000 +246 A 0.000 +247 G 0.000 +248 T 0.000 +249 T 0.000 +250 G 0.000 +251 T 0.000 +252 A 0.000 +253 A 0.000 +254 T 0.000 +255 A 0.000 +256 C 0.000 +257 C 0.000 +258 C 0.000 +259 T 0.000 +260 T 0.000 +261 C 0.000 +262 G 0.000 +263 C 0.000 +264 A 0.000 +265 A 0.000 +266 C 0.000 +267 A 0.000 +268 C 0.000 +269 C 0.000 +270 G 0.000 +271 C 0.000 +272 G 0.000 +273 T 0.000 +274 A 0.000 +275 A 0.000 +276 C 0.000 +277 T 0.000 +278 A 0.000 +279 T 0.000 +280 C 0.000 +281 T 0.000 +282 A 0.000 +283 T 0.000 +284 A 0.000 +285 T 0.000 +286 G 0.000 +287 A 0.000 +288 A 0.000 +289 T 0.000 +290 T 0.000 +291 A 0.000 +292 T 0.000 +293 T 0.000 +294 T 0.000 +295 T 0.000 +296 C 0.000 +297 C 0.000 +298 C 0.000 +299 T 0.000 +300 T 0.000 +301 T 0.000 +302 A 0.000 +303 T 0.000 +304 T 0.000 +305 A 0.000 +306 T 0.000 +307 A 0.000 +308 T 0.000 +309 G 0.000 +310 T 0.000 +311 A 0.000 +312 G 0.000 +313 T 0.000 +314 A 0.000 +315 G 0.000 +316 G 0.000 +317 T 0.000 +318 T 0.000 +319 C 0.000 +320 G 0.000 +321 T 0.000 +322 C 0.000 +323 T 0.000 +324 T 0.000 +325 T 0.000 +326 A 0.000 +327 A 0.000 +328 T 0.000 +329 C 0.000 +330 T 0.000 +331 T 0.000 +332 C 0.000 +333 C 0.000 +334 T 0.000 +335 T 0.000 +336 T 0.000 +337 A 0.000 +338 G 0.000 +339 C 0.000 +340 A 0.000 +341 A 0.000 +342 G 0.000 +343 T 0.000 +344 C 0.000 +345 T 0.000 +346 T 0.000 +347 T 0.000 +348 T 0.000 +349 A 0.000 +350 C 0.000 +351 T 0.000 +352 G 0.000 +353 T 0.000 +354 T 0.000 +355 T 0.000 +356 T 0.000 +357 C 0.000 +358 G 0.000 +359 A 0.000 +360 C 0.000 +361 C 0.000 +362 T 0.000 +363 C 0.000 +364 A 0.000 +365 A 0.000 +366 T 0.000 +367 G 0.000 +368 T 0.000 +369 T 0.000 +370 C 0.000 +371 A 0.000 +372 T 0.000 +373 G 0.000 +374 T 0.000 +375 T 0.000 +376 C 0.000 +377 T 0.000 +378 T 0.000 +379 A 0.000 +380 G 0.000 +381 G 0.000 +382 T 0.000 +383 T 0.000 +384 G 0.000 +385 T 0.000 +386 T 0.000 +387 T 0.000 +388 T 0.000 +389 G 0.000 +390 G 0.000 +391 A 0.000 +392 T 0.000 +393 A 0.000 +394 A 0.000 +395 T 0.000 +396 A 0.000 +397 T 0.000 +398 G 0.000 +399 C 0.000 +400 G 0.000 +401 G 0.000 +402 T 0.000 +403 C 0.000 +404 A 0.000 +405 G 0.000 +406 T 0.000 +407 T 0.000 +408 T 0.000 +409 A 0.000 +410 A 0.000 +411 T 0.000 +412 C 0.000 +413 T 0.000 +414 T 0.000 +415 C 0.000 +416 G 0.000 +417 T 0.000 +418 T 0.000 +419 G 0.000 +420 T 0.000 +421 T 0.000 +422 T 0.000 +423 C 0.000 +424 T 0.000 +425 T 0.000 +426 C 0.000 +427 T 0.000 +428 T 0.000 +429 A 0.000 +430 A 0.000 +431 A 0.000 +432 A 0.000 +433 T 0.000 +434 A 0.000 +435 T 0.000 +436 T 0.000 +437 T 0.000 +438 A 0.000 +439 T 0.000 +440 T 0.000 +441 C 0.000 +442 A 0.000 +443 T 0.000 +444 G 0.000 +445 G 0.000 +446 T 0.000 +447 T 0.000 +448 T 0.000 +449 A 0.000 +450 A 0.000 +451 T 0.000 +452 T 0.000 +453 T 0.000 +454 T 0.000 +455 T 0.000 +456 G 0.000 +457 G 0.000 +458 T 0.000 +459 T 0.000 +460 T 0.000 +461 G 0.000 +462 T 0.000 +463 A 0.000 +464 C 0.000 +465 T 0.000 +466 T 0.000 +467 G 0.000 +468 T 0.000 +469 T 0.000 +470 C 0.000 +471 A 0.000 +472 G 0.000 +473 G 0.000 +474 G 0.000 +475 G 0.000 +476 C 0.000 +477 C 0.000 +478 A 0.000 +479 G 0.000 +480 T 0.000 +481 T 0.000 +482 C 0.000 +483 A 0.000 +484 T 0.000 +485 T 0.000 +486 A 0.000 +487 T 0.000 +488 T 0.000 +489 T 0.000 +490 A 0.000 +491 C 0.000 +492 T 0.000 +493 C 0.000 +494 T 0.000 +495 G 0.000 +496 T 0.000 +497 T 0.000 +498 T 0.000 +499 G 0.000 +500 T 0.000 +501 A 0.000 +502 T 0.000 +503 A 0.000 +504 C 0.000 +505 A 0.000 +506 G 0.000 +507 C 0.000 +508 A 0.000 +509 G 0.000 +510 T 0.000 +511 T 0.000 +512 C 0.000 +513 T 0.000 +514 T 0.000 +515 T 0.000 +516 T 0.000 +517 A 0.000 +518 T 0.000 +519 T 0.000 +520 T 0.000 +521 T 0.000 +522 T 0.000 +523 A 0.000 +524 G 0.000 +525 T 0.000 +526 A 0.000 +527 T 0.000 +528 G 0.000 +529 A 0.000 +530 T 0.000 +531 T 0.000 +532 T 0.000 +533 T 0.000 +534 A 0.000 +535 A 0.000 +536 T 0.000 +537 T 0.000 +538 T 0.000 +539 A 0.000 +540 A 0.000 +541 A 0.000 +542 A 0.000 +543 C 0.000 +544 A 0.000 +545 A 0.000 +546 T 0.000 +547 T 0.000 +548 C 0.000 +549 T 0.000 +550 A 0.000 +551 A 0.000 +552 T 0.000 +553 G 0.000 +554 G 0.000 +555 T 0.000 +556 C 0.000 +557 A 0.000 |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_chips_out.chips --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_chips_out.chips Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,3 @@ +# CHIPS codon usage statistics + +Nc = 61.000 |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_codcmp_out.codcmp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_codcmp_out.codcmp Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,9 @@ +# CODCMP codon usage table comparison +# Ehum.cut vs Eacc.cut + +Sum Squared Difference = 3.044 +Mean Squared Difference = 0.048 +Root Mean Squared Difference = 0.218 +Sum Difference = 11.470 +Mean Difference = 0.179 +Codons not appearing = 0 |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_coderet_out.coderet --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_coderet_out.coderet Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,3 @@ + CDS mRNA non-c Trans Total Sequence + ===== ===== ===== ===== ===== ======== + 0 0 0 0 0 Sequence |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_compseq_out.compseq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_compseq_out.compseq Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,34 @@ +# +# Output from 'compseq' +# +# The Expected frequencies are calculated on the (false) assumption that every +# word has equal frequency. +# +# The input sequences are: +# Sequence + + +Word size 2 +Total count 560 + +# +# Word Obs Count Obs Frequency Exp Frequency Obs/Exp Frequency +# +AA 40 0.0714286 0.0625000 1.1428571 +AC 27 0.0482143 0.0625000 0.7714286 +AG 26 0.0464286 0.0625000 0.7428571 +AT 41 0.0732143 0.0625000 1.1714286 +CA 26 0.0464286 0.0625000 0.7428571 +CC 24 0.0428571 0.0625000 0.6857143 +CG 15 0.0267857 0.0625000 0.4285714 +CT 41 0.0732143 0.0625000 1.1714286 +GA 19 0.0339286 0.0625000 0.5428571 +GC 17 0.0303571 0.0625000 0.4857143 +GG 19 0.0339286 0.0625000 0.5428571 +GT 43 0.0767857 0.0625000 1.2285714 +TA 50 0.0892857 0.0625000 1.4285714 +TC 38 0.0678571 0.0625000 1.0857143 +TG 37 0.0660714 0.0625000 1.0571429 +TT 97 0.1732143 0.0625000 2.7714286 + +Other 0 0.0000000 0.0000000 10000000000.0000000 |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_cpgreport_out1.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_cpgreport_out1.gff Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,13 @@ +##gff-version 2.0 +##date 2007-10-15 +##Type DNA Sequence +Sequence cpgreport misc_feature 4 5 17.000 + . Sequence "Sequence.1" +Sequence cpgreport misc_feature 66 67 17.000 + . Sequence "Sequence.2" +Sequence cpgreport misc_feature 101 102 17.000 + . Sequence "Sequence.3" +Sequence cpgreport misc_feature 121 141 34.000 + . Sequence "Sequence.4" +Sequence cpgreport misc_feature 185 186 17.000 + . Sequence "Sequence.5" +Sequence cpgreport misc_feature 209 210 17.000 + . Sequence "Sequence.6" +Sequence cpgreport misc_feature 261 272 43.000 + . Sequence "Sequence.7" +Sequence cpgreport misc_feature 319 320 17.000 + . Sequence "Sequence.8" +Sequence cpgreport misc_feature 357 358 17.000 + . Sequence "Sequence.9" +Sequence cpgreport misc_feature 399 416 19.000 + . Sequence "Sequence.10" |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_cpgreport_out2.cpgreport --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_cpgreport_out2.cpgreport Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,15 @@ + + +CPGREPORT of Sequence from 1 to 561 + +Sequence Begin End Score CpG %CG CG/GC +Sequence 4 5 17 1 100.0 - +Sequence 66 67 17 1 100.0 - +Sequence 101 102 17 1 100.0 - +Sequence 121 141 34 3 57.1 1.00 +Sequence 185 186 17 1 100.0 - +Sequence 209 210 17 1 100.0 - +Sequence 261 272 43 3 75.0 1.00 +Sequence 319 320 17 1 100.0 - +Sequence 357 358 17 1 100.0 - +Sequence 399 416 19 2 44.4 - |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_cusp_out.cusp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_cusp_out.cusp Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,72 @@ +#CdsCount: 10 + +#Coding GC 36.36% +#1st letter GC 34.22% +#2nd letter GC 35.29% +#3rd letter GC 39.57% + +#Codon AA Fraction Frequency Number +GCA A 0.200 5.348 1 +GCC A 0.400 10.695 2 +GCG A 0.400 10.695 2 +GCT A 0.000 0.000 0 +TGC C 0.500 21.390 4 +TGT C 0.500 21.390 4 +GAC D 0.667 10.695 2 +GAT D 0.333 5.348 1 +GAA E 0.500 5.348 1 +GAG E 0.500 5.348 1 +TTC F 0.316 32.086 6 +TTT F 0.684 69.519 13 +GGA G 0.000 0.000 0 +GGC G 0.200 5.348 1 +GGG G 0.200 5.348 1 +GGT G 0.600 16.043 3 +CAC H 0.667 10.695 2 +CAT H 0.333 5.348 1 +ATA I 0.429 16.043 3 +ATC I 0.143 5.348 1 +ATT I 0.429 16.043 3 +AAA K 0.600 32.086 6 +AAG K 0.400 21.390 4 +CTA L 0.152 26.738 5 +CTC L 0.061 10.695 2 +CTG L 0.152 26.738 5 +CTT L 0.273 48.128 9 +TTA L 0.182 32.086 6 +TTG L 0.182 32.086 6 +ATG M 1.000 16.043 3 +AAC N 0.286 10.695 2 +AAT N 0.714 26.738 5 +CCA P 0.250 5.348 1 +CCC P 0.500 10.695 2 +CCG P 0.250 5.348 1 +CCT P 0.000 0.000 0 +CAA Q 0.333 5.348 1 +CAG Q 0.667 10.695 2 +AGA R 0.143 5.348 1 +AGG R 0.143 5.348 1 +CGA R 0.143 5.348 1 +CGC R 0.000 0.000 0 +CGG R 0.143 5.348 1 +CGT R 0.429 16.043 3 +AGC S 0.136 16.043 3 +AGT S 0.227 26.738 5 +TCA S 0.136 16.043 3 +TCC S 0.227 26.738 5 +TCG S 0.000 0.000 0 +TCT S 0.273 32.086 6 +ACA T 0.400 21.390 4 +ACC T 0.100 5.348 1 +ACG T 0.200 10.695 2 +ACT T 0.300 16.043 3 +GTA V 0.231 16.043 3 +GTC V 0.000 0.000 0 +GTG V 0.000 0.000 0 +GTT V 0.769 53.476 10 +TGG W 1.000 21.390 4 +TAC Y 0.444 21.390 4 +TAT Y 0.556 26.738 5 +TAA * 0.500 26.738 5 +TAG * 0.400 21.390 4 +TGA * 0.100 5.348 1 |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_cutseq_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_cutseq_out.fasta Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,11 @@ +>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +ttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggcttt +acaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttacc +ggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgga +agacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactgg +atacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttcccttt +attatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgacc +tcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgtt +tcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagtt +cattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaaa +acaattctaatggtcaaaaa |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_dan_out.png |
| b |
| Binary file test-data/emboss_dan_out.png has changed |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_degapseq_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_degapseq_out.fasta Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,11 @@ +>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt +tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac +cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg +aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg +gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt +tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac +ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt +ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt +tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa +aacaattctaatggtcaaaaa |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_descseq_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_descseq_out.fasta Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,11 @@ +>Sequencetest 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;test +gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt +tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac +cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg +aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg +gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt +tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac +ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt +ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt +tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa +aacaattctaatggtcaaaaa |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_einverted_out.einverted --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_einverted_out.einverted Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,20 @@ + +hg17: Score 97: 63/77 ( 81%) matches, 3 gaps + 2684 gtggcaggctcggttcaccaacgtcatttgcagttccccgctttatgttatggg-t--tttgttttgttttgtttttttt 2760 + |||| |||| | |||||| || |||| |||||||||||||| | ||||| | |||||||||||||||||| ||| + 3298 caccatccgtacaaagtggacatagcaaacatcaaggggcgaaatgtactacccaaccaaacaaaacaaaacaaaacaaa 3219 + +hg17: Score 94: 34/36 ( 94%) matches, 0 gaps + 7058 gacacacacacacacacacacacacacacacacaca 7093 + |||||||| ||||||||||| ||||||||||||||| + 7888 ctgtgtgtatgtgtgtgtgtctgtgtgtgtgtgtgt 7853 + +hg17: Score 139: 213/305 ( 69%) matches, 11 gaps + 8604 ggtggctcatgcctgtaatcccagcattttgggaggccgaggcgggtggatcac--gaggtcaggagtttgagaccagcctggccaagatggtgaagcctcgtctctactaaaaatacaaa-aattagccaggt-gcggtg-gtgggcgcctgtatttccagctacccgggaggctgaggaggctgaggcaggagaatcgcttgaacccgggaggcggaggttgcagtgagccgaggtcacgccactgcactctagcctgggcaacagagcaagactccgtcaaaaaaaaaataaaaaaataaaaaaataaaaaaa 8914 + ||||||||| |||| ||||||||| ||||||||||| |||| || ||||| | ||| |||||||| |||||||||||| | | | | | || | |||||| ||||||| ||| || | | | || | | |||| || || | | ||| | || |||||| ||| |||| | || ||| ||| ||| | |||| ||||||||| | |||| || ||||||| |||||| | ||| |||||||| || || ||||| |||| ||||| |||| ||| + 9563 ccaccgagt-cggatattagggtcccgaaaccctccggttccgtcctcctagcgaactcgggtcctcaagttctggtcggacccgctgtgtcgttctggggtagagattttttttatttttatttttatttttatcgactcacaccaccgtttgcgaa-cacca-ggg-tcgatgaaccctccggttccaccctccaaacggactcgggtcctacagctccgacgtcactccatactagtg-tgtcacgtgaggtcggacacactgtgtcgttctggggtag-agaatttttgttttcggttttttctattacttt 9254 + +hg17: Score 202: 70/72 ( 97%) matches, 0 gaps + 18075 tgcattttattctggatggatttgaagcaaagcaccagcttctccaggctctttggggtcagccagggccag 18146 + ||| |||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||| + 18677 acgcaaaataagacctacctaaacttcgtttcgtagtcgaagaggtccgagaaaccccagtcggtcccggtc 18606 |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_epestfind_out.epestfind --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_epestfind_out.epestfind Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,41 @@ +PEST-find: Finds PEST motifs as potential proteolytic cleavage sites. + + No PEST motif was identified in Sequence from 1 to 561. + + + ---------+---------+---------+---------+---------+---------+ + + 1 GTTCGATGCCTAAAATACCTTCTTTTGTCCCTACACAGACCACAGTTTTCCTAATGGCTT 60 + + + 61 TACACCGACTAGAAATTCTTGTGCAAGCACTAATTGAAAGCGGTTGGCCTAGAGTGTTAC 120 + + + 121 CGGTTTGTATAGCTGAGCGCGTCTCTTGCCCTGATCAAAGGTTCATTTTCTCTACTTTGG 180 + + + 181 AAGACGTTGTGGAAGAATACAACAAGTACGAGTCTCTCCCCCCTGGTTTGCTGATTACTG 240 + + + 241 GATACAGTTGTAATACCCTTCGCAACACCGCGTAACTATCTATATGAATTATTTTCCCTT 300 + + + 301 TATTATATGTAGTAGGTTCGTCTTTAATCTTCCTTTAGCAAGTCTTTTACTGTTTTCGAC 360 + + + 361 CTCAATGTTCATGTTCTTAGGTTGTTTTGGATAATATGCGGTCAGTTTAATCTTCGTTGT 420 + + + 421 TTCTTCTTAAAATATTTATTCATGGTTTAATTTTTGGTTTGTACTTGTTCAGGGGCCAGT 480 + + + 481 TCATTATTTACTCTGTTTGTATACAGCAGTTCTTTTATTTTTAGTATGATTTTAATTTAA 540 + + + 541 AACAATTCTAATGGTCAAAAA 561 + + + Symbols PEST motifs + +++++++ potential + OOOOOOO poor + |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_equicktandem_out.equicktandem --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_equicktandem_out.equicktandem Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,16 @@ + 22 8881 8915 1 35 + 33 7059 7093 2 17 + 29 7847 7891 2 22 + 27 3213 3248 5 7 + 20 9430 9457 6 4 + 39 19631 19709 36 2 + 39 19851 19927 36 2 + 37 20067 20141 36 2 + 21 19550 19630 60 1 + 21 19770 19850 60 1 + 79 19928 20066 60 2 + 24 8595 8793 133 1 + 26 2844 3045 134 1 + 35 10945 11179 136 1 + 22 15264 15435 138 1 + 29 11181 11429 168 1 |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_est2genome_out.est2genome --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_est2genome_out.est2genome Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,1 @@ +Note Best alignment is between reversed est and forward genome, and splice sites imply forward gene |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_etandem_out.table --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_etandem_out.table Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,2 @@ + 24 7847 7886 10 4 92.5 tgtgtgtgtg + 22 7059 7098 10 4 90.0 acacacacac |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_extractseq_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_extractseq_out.fasta Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,11 @@ +>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt +tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac +cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg +aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg +gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt +tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac +ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt +ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt +tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa +aacaattctaatggtcaaaaa |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_freak_out.freak --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_freak_out.freak Wed Mar 21 16:30:01 2012 -0400 |
| b |
| b'@@ -0,0 +1,534 @@\n+FREAK of Sequence from 1 to 561 Window 30 Step 1\n+\n+1 0.400000\n+2 0.400000\n+3 0.400000\n+4 0.400000\n+5 0.400000\n+6 0.366667\n+7 0.400000\n+8 0.400000\n+9 0.400000\n+10 0.366667\n+11 0.366667\n+12 0.400000\n+13 0.400000\n+14 0.433333\n+15 0.433333\n+16 0.466667\n+17 0.466667\n+18 0.466667\n+19 0.433333\n+20 0.400000\n+21 0.433333\n+22 0.466667\n+23 0.433333\n+24 0.433333\n+25 0.433333\n+26 0.433333\n+27 0.466667\n+28 0.466667\n+29 0.500000\n+30 0.466667\n+31 0.433333\n+32 0.400000\n+33 0.400000\n+34 0.433333\n+35 0.400000\n+36 0.433333\n+37 0.433333\n+38 0.466667\n+39 0.433333\n+40 0.466667\n+41 0.433333\n+42 0.400000\n+43 0.433333\n+44 0.400000\n+45 0.400000\n+46 0.366667\n+47 0.366667\n+48 0.366667\n+49 0.400000\n+50 0.400000\n+51 0.366667\n+52 0.366667\n+53 0.366667\n+54 0.400000\n+55 0.433333\n+56 0.433333\n+57 0.400000\n+58 0.400000\n+59 0.400000\n+60 0.400000\n+61 0.433333\n+62 0.433333\n+63 0.433333\n+64 0.400000\n+65 0.400000\n+66 0.366667\n+67 0.366667\n+68 0.333333\n+69 0.333333\n+70 0.300000\n+71 0.333333\n+72 0.366667\n+73 0.366667\n+74 0.400000\n+75 0.400000\n+76 0.400000\n+77 0.433333\n+78 0.466667\n+79 0.466667\n+80 0.500000\n+81 0.500000\n+82 0.466667\n+83 0.500000\n+84 0.466667\n+85 0.466667\n+86 0.466667\n+87 0.500000\n+88 0.466667\n+89 0.433333\n+90 0.433333\n+91 0.433333\n+92 0.466667\n+93 0.500000\n+94 0.533333\n+95 0.533333\n+96 0.533333\n+97 0.500000\n+98 0.533333\n+99 0.533333\n+100 0.533333\n+101 0.500000\n+102 0.466667\n+103 0.466667\n+104 0.466667\n+105 0.466667\n+106 0.500000\n+107 0.466667\n+108 0.466667\n+109 0.466667\n+110 0.466667\n+111 0.500000\n+112 0.533333\n+113 0.500000\n+114 0.533333\n+115 0.500000\n+116 0.533333\n+117 0.500000\n+118 0.500000\n+119 0.533333\n+120 0.566667\n+121 0.566667\n+122 0.566667\n+123 0.533333\n+124 0.533333\n+125 0.533333\n+126 0.533333\n+127 0.566667\n+128 0.533333\n+129 0.533333\n+130 0.533333\n+131 0.566667\n+132 0.600000\n+133 0.566667\n+134 0.533333\n+135 0.566667\n+136 0.533333\n+137 0.533333\n+138 0.500000\n+139 0.466667\n+140 0.433333\n+141 0.433333\n+142 0.400000\n+143 0.433333\n+144 0.400000\n+145 0.400000\n+146 0.400000\n+147 0.400000\n+148 0.400000\n+149 0.366667\n+150 0.366667\n+151 0.366667\n+152 0.333333\n+153 0.333333\n+154 0.333333\n+155 0.333333\n+156 0.366667\n+157 0.366667\n+158 0.366667\n+159 0.366667\n+160 0.400000\n+161 0.366667\n+162 0.366667\n+163 0.400000\n+164 0.400000\n+165 0.366667\n+166 0.400000\n+167 0.400000\n+168 0.400000\n+169 0.400000\n+170 0.400000\n+171 0.400000\n+172 0.400000\n+173 0.366667\n+174 0.400000\n+175 0.400000\n+176 0.366667\n+177 0.400000\n+178 0.400000\n+179 0.400000\n+180 0.400000\n+181 0.400000\n+182 0.400000\n+183 0.433333\n+184 0.400000\n+185 0.433333\n+186 0.400000\n+187 0.400000\n+1'..b'0.366667\n+343 0.333333\n+344 0.366667\n+345 0.333333\n+346 0.333333\n+347 0.366667\n+348 0.366667\n+349 0.366667\n+350 0.366667\n+351 0.366667\n+352 0.400000\n+353 0.366667\n+354 0.366667\n+355 0.400000\n+356 0.400000\n+357 0.400000\n+358 0.366667\n+359 0.333333\n+360 0.366667\n+361 0.366667\n+362 0.333333\n+363 0.333333\n+364 0.300000\n+365 0.300000\n+366 0.300000\n+367 0.300000\n+368 0.266667\n+369 0.300000\n+370 0.333333\n+371 0.333333\n+372 0.366667\n+373 0.366667\n+374 0.366667\n+375 0.366667\n+376 0.400000\n+377 0.366667\n+378 0.366667\n+379 0.366667\n+380 0.366667\n+381 0.333333\n+382 0.300000\n+383 0.333333\n+384 0.333333\n+385 0.300000\n+386 0.333333\n+387 0.366667\n+388 0.366667\n+389 0.366667\n+390 0.366667\n+391 0.333333\n+392 0.333333\n+393 0.333333\n+394 0.366667\n+395 0.366667\n+396 0.366667\n+397 0.400000\n+398 0.400000\n+399 0.366667\n+400 0.333333\n+401 0.300000\n+402 0.266667\n+403 0.266667\n+404 0.233333\n+405 0.233333\n+406 0.200000\n+407 0.200000\n+408 0.200000\n+409 0.200000\n+410 0.200000\n+411 0.200000\n+412 0.233333\n+413 0.200000\n+414 0.200000\n+415 0.233333\n+416 0.233333\n+417 0.200000\n+418 0.200000\n+419 0.200000\n+420 0.166667\n+421 0.166667\n+422 0.166667\n+423 0.166667\n+424 0.133333\n+425 0.133333\n+426 0.133333\n+427 0.133333\n+428 0.166667\n+429 0.166667\n+430 0.166667\n+431 0.166667\n+432 0.200000\n+433 0.200000\n+434 0.200000\n+435 0.233333\n+436 0.233333\n+437 0.233333\n+438 0.266667\n+439 0.266667\n+440 0.266667\n+441 0.300000\n+442 0.266667\n+443 0.300000\n+444 0.333333\n+445 0.333333\n+446 0.333333\n+447 0.366667\n+448 0.400000\n+449 0.400000\n+450 0.433333\n+451 0.433333\n+452 0.433333\n+453 0.466667\n+454 0.466667\n+455 0.466667\n+456 0.466667\n+457 0.433333\n+458 0.400000\n+459 0.400000\n+460 0.400000\n+461 0.400000\n+462 0.400000\n+463 0.400000\n+464 0.433333\n+465 0.400000\n+466 0.433333\n+467 0.433333\n+468 0.400000\n+469 0.400000\n+470 0.433333\n+471 0.400000\n+472 0.400000\n+473 0.366667\n+474 0.333333\n+475 0.333333\n+476 0.300000\n+477 0.300000\n+478 0.300000\n+479 0.300000\n+480 0.300000\n+481 0.300000\n+482 0.300000\n+483 0.300000\n+484 0.300000\n+485 0.300000\n+486 0.300000\n+487 0.300000\n+488 0.300000\n+489 0.300000\n+490 0.300000\n+491 0.300000\n+492 0.266667\n+493 0.266667\n+494 0.233333\n+495 0.266667\n+496 0.233333\n+497 0.233333\n+498 0.233333\n+499 0.266667\n+500 0.233333\n+501 0.233333\n+502 0.233333\n+503 0.233333\n+504 0.233333\n+505 0.200000\n+506 0.200000\n+507 0.166667\n+508 0.133333\n+509 0.133333\n+510 0.100000\n+511 0.100000\n+512 0.100000\n+513 0.066667\n+514 0.100000\n+515 0.100000\n+516 0.100000\n+517 0.100000\n+518 0.100000\n+519 0.133333\n+520 0.133333\n+521 0.133333\n+522 0.133333\n+523 0.133333\n+524 0.166667\n+525 0.166667\n+526 0.166667\n+527 0.200000\n+528 0.200000\n+529 0.166667\n+530 0.166667\n+531 0.166667\n+532 0.166667\n' |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_fuzznuc_out.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_fuzznuc_out.tabular Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,41 @@ +SeqName Start End Score Strand Pattern_name Mismatch +Sequence 12 13 2 + pattern1 . +Sequence 13 14 2 + pattern1 . +Sequence 14 15 2 + pattern1 . +Sequence 53 54 2 + pattern1 . +Sequence 73 74 2 + pattern1 . +Sequence 74 75 2 + pattern1 . +Sequence 85 86 2 + pattern1 . +Sequence 92 93 2 + pattern1 . +Sequence 97 98 2 + pattern1 . +Sequence 98 99 2 + pattern1 . +Sequence 157 158 2 + pattern1 . +Sequence 158 159 2 + pattern1 . +Sequence 181 182 2 + pattern1 . +Sequence 193 194 2 + pattern1 . +Sequence 196 197 2 + pattern1 . +Sequence 201 202 2 + pattern1 . +Sequence 204 205 2 + pattern1 . +Sequence 252 253 2 + pattern1 . +Sequence 264 265 2 + pattern1 . +Sequence 274 275 2 + pattern1 . +Sequence 287 288 2 + pattern1 . +Sequence 326 327 2 + pattern1 . +Sequence 340 341 2 + pattern1 . +Sequence 364 365 2 + pattern1 . +Sequence 393 394 2 + pattern1 . +Sequence 409 410 2 + pattern1 . +Sequence 429 430 2 + pattern1 . +Sequence 430 431 2 + pattern1 . +Sequence 431 432 2 + pattern1 . +Sequence 449 450 2 + pattern1 . +Sequence 534 535 2 + pattern1 . +Sequence 539 540 2 + pattern1 . +Sequence 540 541 2 + pattern1 . +Sequence 541 542 2 + pattern1 . +Sequence 544 545 2 + pattern1 . +Sequence 550 551 2 + pattern1 . +Sequence 557 558 2 + pattern1 . +Sequence 558 559 2 + pattern1 . +Sequence 559 560 2 + pattern1 . +Sequence 560 561 2 + pattern1 . |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_fuzzpro_out.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_fuzzpro_out.tabular Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,41 @@ +SeqName Start End Score Strand Pattern_name Mismatch +Sequence 12 13 2 + pattern1 . +Sequence 13 14 2 + pattern1 . +Sequence 14 15 2 + pattern1 . +Sequence 53 54 2 + pattern1 . +Sequence 73 74 2 + pattern1 . +Sequence 74 75 2 + pattern1 . +Sequence 85 86 2 + pattern1 . +Sequence 92 93 2 + pattern1 . +Sequence 97 98 2 + pattern1 . +Sequence 98 99 2 + pattern1 . +Sequence 157 158 2 + pattern1 . +Sequence 158 159 2 + pattern1 . +Sequence 181 182 2 + pattern1 . +Sequence 193 194 2 + pattern1 . +Sequence 196 197 2 + pattern1 . +Sequence 201 202 2 + pattern1 . +Sequence 204 205 2 + pattern1 . +Sequence 252 253 2 + pattern1 . +Sequence 264 265 2 + pattern1 . +Sequence 274 275 2 + pattern1 . +Sequence 287 288 2 + pattern1 . +Sequence 326 327 2 + pattern1 . +Sequence 340 341 2 + pattern1 . +Sequence 364 365 2 + pattern1 . +Sequence 393 394 2 + pattern1 . +Sequence 409 410 2 + pattern1 . +Sequence 429 430 2 + pattern1 . +Sequence 430 431 2 + pattern1 . +Sequence 431 432 2 + pattern1 . +Sequence 449 450 2 + pattern1 . +Sequence 534 535 2 + pattern1 . +Sequence 539 540 2 + pattern1 . +Sequence 540 541 2 + pattern1 . +Sequence 541 542 2 + pattern1 . +Sequence 544 545 2 + pattern1 . +Sequence 550 551 2 + pattern1 . +Sequence 557 558 2 + pattern1 . +Sequence 558 559 2 + pattern1 . +Sequence 559 560 2 + pattern1 . +Sequence 560 561 2 + pattern1 . |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_fuzztran_out.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_fuzztran_out.tabular Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,133 @@ +SeqName Start End Score Strand Pattern_name Mismatch Frame PStart PEnd Translation +hg17 3958 3963 2 + pattern1 . 1 1320 1321 AA +hg17 3961 3966 2 + pattern1 . 1 1321 1322 AA +hg17 4099 4104 2 + pattern1 . 1 1367 1368 AA +hg17 4315 4320 2 + pattern1 . 1 1439 1440 AA +hg17 5194 5199 2 + pattern1 . 1 1732 1733 AA +hg17 8584 8589 2 + pattern1 . 1 2862 2863 AA +hg17 9232 9237 2 + pattern1 . 1 3078 3079 AA +hg17 9343 9348 2 + pattern1 . 1 3115 3116 AA +hg17 9715 9720 2 + pattern1 . 1 3239 3240 AA +hg17 9769 9774 2 + pattern1 . 1 3257 3258 AA +hg17 9841 9846 2 + pattern1 . 1 3281 3282 AA +hg17 9994 9999 2 + pattern1 . 1 3332 3333 AA +hg17 10045 10050 2 + pattern1 . 1 3349 3350 AA +hg17 10048 10053 2 + pattern1 . 1 3350 3351 AA +hg17 12157 12162 2 + pattern1 . 1 4053 4054 AA +hg17 12487 12492 2 + pattern1 . 1 4163 4164 AA +hg17 12688 12693 2 + pattern1 . 1 4230 4231 AA +hg17 12691 12696 2 + pattern1 . 1 4231 4232 AA +hg17 15010 15015 2 + pattern1 . 1 5004 5005 AA +hg17 17521 17526 2 + pattern1 . 1 5841 5842 AA +hg17 17551 17556 2 + pattern1 . 1 5851 5852 AA +hg17 1148 1153 2 + pattern1 . 2 383 384 AA +hg17 2078 2083 2 + pattern1 . 2 693 694 AA +hg17 2432 2437 2 + pattern1 . 2 811 812 AA +hg17 3080 3085 2 + pattern1 . 2 1027 1028 AA +hg17 3593 3598 2 + pattern1 . 2 1198 1199 AA +hg17 3692 3697 2 + pattern1 . 2 1231 1232 AA +hg17 4055 4060 2 + pattern1 . 2 1352 1353 AA +hg17 5018 5023 2 + pattern1 . 2 1673 1674 AA +hg17 5147 5152 2 + pattern1 . 2 1716 1717 AA +hg17 8276 8281 2 + pattern1 . 2 2759 2760 AA +hg17 9587 9592 2 + pattern1 . 2 3196 3197 AA +hg17 9668 9673 2 + pattern1 . 2 3223 3224 AA +hg17 9920 9925 2 + pattern1 . 2 3307 3308 AA +hg17 9971 9976 2 + pattern1 . 2 3324 3325 AA +hg17 10112 10117 2 + pattern1 . 2 3371 3372 AA +hg17 10115 10120 2 + pattern1 . 2 3372 3373 AA +hg17 11837 11842 2 + pattern1 . 2 3946 3947 AA +hg17 12026 12031 2 + pattern1 . 2 4009 4010 AA +hg17 12944 12949 2 + pattern1 . 2 4315 4316 AA +hg17 12953 12958 2 + pattern1 . 2 4318 4319 AA +hg17 13229 13234 2 + pattern1 . 2 4410 4411 AA +hg17 13232 13237 2 + pattern1 . 2 4411 4412 AA +hg17 15356 15361 2 + pattern1 . 2 5119 5120 AA +hg17 15482 15487 2 + pattern1 . 2 5161 5162 AA +hg17 16061 16066 2 + pattern1 . 2 5354 5355 AA +hg17 17822 17827 2 + pattern1 . 2 5941 5942 AA +hg17 15 20 2 + pattern1 . 3 5 6 AA +hg17 33 38 2 + pattern1 . 3 11 12 AA +hg17 3669 3674 2 + pattern1 . 3 1223 1224 AA +hg17 3759 3764 2 + pattern1 . 3 1253 1254 AA +hg17 5646 5651 2 + pattern1 . 3 1882 1883 AA +hg17 5847 5852 2 + pattern1 . 3 1949 1950 AA +hg17 5850 5855 2 + pattern1 . 3 1950 1951 AA +hg17 5853 5858 2 + pattern1 . 3 1951 1952 AA +hg17 7674 7679 2 + pattern1 . 3 2558 2559 AA +hg17 9699 9704 2 + pattern1 . 3 3233 3234 AA +hg17 9891 9896 2 + pattern1 . 3 3297 3298 AA +hg17 10074 10079 2 + pattern1 . 3 3358 3359 AA +hg17 10407 10412 2 + pattern1 . 3 3469 3470 AA +hg17 12675 12680 2 + pattern1 . 3 4225 4226 AA +hg17 13746 13751 2 + pattern1 . 3 4582 4583 AA +hg17 17115 17120 2 + pattern1 . 3 5705 5706 AA +hg17 17421 17426 2 + pattern1 . 3 5807 5808 AA +hg17 19122 19127 2 + pattern1 . 3 6374 6375 AA +hg17 19353 19358 2 + pattern1 . 3 6451 6452 AA +hg17 -2312 -2317 2 - pattern1 . 1 772 773 AA +hg17 -4073 -4078 2 - pattern1 . 1 1359 1360 AA +hg17 -4652 -4657 2 - pattern1 . 1 1552 1553 AA +hg17 -4778 -4783 2 - pattern1 . 1 1594 1595 AA +hg17 -6902 -6907 2 - pattern1 . 1 2302 2303 AA +hg17 -6905 -6910 2 - pattern1 . 1 2303 2304 AA +hg17 -7181 -7186 2 - pattern1 . 1 2395 2396 AA +hg17 -7190 -7195 2 - pattern1 . 1 2398 2399 AA +hg17 -8108 -8113 2 - pattern1 . 1 2704 2705 AA +hg17 -8297 -8302 2 - pattern1 . 1 2767 2768 AA +hg17 -10019 -10024 2 - pattern1 . 1 3341 3342 AA +hg17 -10022 -10027 2 - pattern1 . 1 3342 3343 AA +hg17 -10163 -10168 2 - pattern1 . 1 3389 3390 AA +hg17 -10214 -10219 2 - pattern1 . 1 3406 3407 AA +hg17 -10466 -10471 2 - pattern1 . 1 3490 3491 AA +hg17 -10547 -10552 2 - pattern1 . 1 3517 3518 AA +hg17 -11858 -11863 2 - pattern1 . 1 3954 3955 AA +hg17 -14987 -14992 2 - pattern1 . 1 4997 4998 AA +hg17 -15116 -15121 2 - pattern1 . 1 5040 5041 AA +hg17 -16079 -16084 2 - pattern1 . 1 5361 5362 AA +hg17 -16442 -16447 2 - pattern1 . 1 5482 5483 AA +hg17 -16541 -16546 2 - pattern1 . 1 5515 5516 AA +hg17 -17054 -17059 2 - pattern1 . 1 5686 5687 AA +hg17 -17702 -17707 2 - pattern1 . 1 5902 5903 AA +hg17 -18056 -18061 2 - pattern1 . 1 6020 6021 AA +hg17 -18986 -18991 2 - pattern1 . 1 6330 6331 AA +hg17 -783 -788 2 - pattern1 . 2 262 263 AA +hg17 -1014 -1019 2 - pattern1 . 2 339 340 AA +hg17 -2715 -2720 2 - pattern1 . 2 906 907 AA +hg17 -3021 -3026 2 - pattern1 . 2 1008 1009 AA +hg17 -6390 -6395 2 - pattern1 . 2 2131 2132 AA +hg17 -7461 -7466 2 - pattern1 . 2 2488 2489 AA +hg17 -9729 -9734 2 - pattern1 . 2 3244 3245 AA +hg17 -10062 -10067 2 - pattern1 . 2 3355 3356 AA +hg17 -10245 -10250 2 - pattern1 . 2 3416 3417 AA +hg17 -10437 -10442 2 - pattern1 . 2 3480 3481 AA +hg17 -12462 -12467 2 - pattern1 . 2 4155 4156 AA +hg17 -14283 -14288 2 - pattern1 . 2 4762 4763 AA +hg17 -14286 -14291 2 - pattern1 . 2 4763 4764 AA +hg17 -14289 -14294 2 - pattern1 . 2 4764 4765 AA +hg17 -14490 -14495 2 - pattern1 . 2 4831 4832 AA +hg17 -16377 -16382 2 - pattern1 . 2 5460 5461 AA +hg17 -16467 -16472 2 - pattern1 . 2 5490 5491 AA +hg17 -20103 -20108 2 - pattern1 . 2 6702 6703 AA +hg17 -20121 -20126 2 - pattern1 . 2 6708 6709 AA +hg17 17553 17548 2 - pattern1 . 3 863 864 AA +hg17 17523 17518 2 - pattern1 . 3 873 874 AA +hg17 15012 15007 2 - pattern1 . 3 1710 1711 AA +hg17 12693 12688 2 - pattern1 . 3 2483 2484 AA +hg17 12690 12685 2 - pattern1 . 3 2484 2485 AA +hg17 12489 12484 2 - pattern1 . 3 2551 2552 AA +hg17 12159 12154 2 - pattern1 . 3 2661 2662 AA +hg17 10050 10045 2 - pattern1 . 3 3364 3365 AA +hg17 10047 10042 2 - pattern1 . 3 3365 3366 AA +hg17 9996 9991 2 - pattern1 . 3 3382 3383 AA +hg17 9843 9838 2 - pattern1 . 3 3433 3434 AA +hg17 9771 9766 2 - pattern1 . 3 3457 3458 AA +hg17 9717 9712 2 - pattern1 . 3 3475 3476 AA +hg17 9345 9340 2 - pattern1 . 3 3599 3600 AA +hg17 9234 9229 2 - pattern1 . 3 3636 3637 AA +hg17 8586 8581 2 - pattern1 . 3 3852 3853 AA +hg17 5196 5191 2 - pattern1 . 3 4982 4983 AA +hg17 4317 4312 2 - pattern1 . 3 5275 5276 AA +hg17 4101 4096 2 - pattern1 . 3 5347 5348 AA +hg17 3963 3958 2 - pattern1 . 3 5393 5394 AA +hg17 3960 3955 2 - pattern1 . 3 5394 5395 AA |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_garnier_out.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_garnier_out.tabular Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,102 @@ +SeqName Start End Score Strand helix sheet turns coil +Sequence 1 9 0.000 + . . T . +Sequence 10 10 0.000 + . E . . +Sequence 11 16 0.000 + H . . . +Sequence 17 39 0.000 + . . T . +Sequence 40 40 0.000 + H . . . +Sequence 41 42 0.000 + . E . . +Sequence 43 48 0.000 + . . T . +Sequence 49 52 0.000 + . E . . +Sequence 53 68 0.000 + . . T . +Sequence 69 75 0.000 + H . . . +Sequence 76 78 0.000 + . E . . +Sequence 79 87 0.000 + . . T . +Sequence 88 90 0.000 + . E . . +Sequence 91 96 0.000 + H . . . +Sequence 97 98 0.000 + . E . . +Sequence 99 99 0.000 + . . . C +Sequence 100 107 0.000 + . . T . +Sequence 108 111 0.000 + . E . . +Sequence 112 116 0.000 + . . T . +Sequence 117 120 0.000 + . E . . +Sequence 121 123 0.000 + . . T . +Sequence 124 126 0.000 + . . . C +Sequence 127 131 0.000 + . E . . +Sequence 132 153 0.000 + . . T . +Sequence 154 157 0.000 + . E . . +Sequence 158 161 0.000 + . . T . +Sequence 162 162 0.000 + . . . C +Sequence 163 164 0.000 + . E . . +Sequence 165 172 0.000 + . . T . +Sequence 173 176 0.000 + . E . . +Sequence 177 180 0.000 + . . T . +Sequence 181 183 0.000 + . . . C +Sequence 184 187 0.000 + . E . . +Sequence 188 194 0.000 + . . . C +Sequence 195 206 0.000 + H . . . +Sequence 207 234 0.000 + . . T . +Sequence 235 237 0.000 + . E . . +Sequence 238 241 0.000 + . . T . +Sequence 242 242 0.000 + . . . C +Sequence 243 246 0.000 + . E . . +Sequence 247 247 0.000 + . . T . +Sequence 248 249 0.000 + . . . C +Sequence 250 275 0.000 + . . T . +Sequence 276 282 0.000 + . E . . +Sequence 283 283 0.000 + H . . . +Sequence 284 289 0.000 + . . . C +Sequence 290 301 0.000 + . . T . +Sequence 302 307 0.000 + . E . . +Sequence 308 313 0.000 + . . . C +Sequence 314 321 0.000 + . . T . +Sequence 322 322 0.000 + . E . . +Sequence 323 344 0.000 + . . T . +Sequence 345 348 0.000 + . E . . +Sequence 349 360 0.000 + . . T . +Sequence 361 363 0.000 + . E . . +Sequence 364 374 0.000 + . . T . +Sequence 375 378 0.000 + . E . . +Sequence 379 381 0.000 + . . T . +Sequence 382 384 0.000 + . . . C +Sequence 385 386 0.000 + . E . . +Sequence 387 392 0.000 + . . . C +Sequence 393 396 0.000 + . E . . +Sequence 397 401 0.000 + . . T . +Sequence 402 402 0.000 + . . . C +Sequence 403 403 0.000 + . E . . +Sequence 404 406 0.000 + . . T . +Sequence 407 407 0.000 + . . . C +Sequence 408 409 0.000 + . . T . +Sequence 410 412 0.000 + . E . . +Sequence 413 422 0.000 + . . T . +Sequence 423 427 0.000 + . E . . +Sequence 428 436 0.000 + H . . . +Sequence 437 441 0.000 + . E . . +Sequence 442 444 0.000 + . . T . +Sequence 445 447 0.000 + . . . C +Sequence 448 452 0.000 + . E . . +Sequence 453 455 0.000 + . . . C +Sequence 456 457 0.000 + . . T . +Sequence 458 460 0.000 + . . . C +Sequence 461 463 0.000 + . E . . +Sequence 464 467 0.000 + . . T . +Sequence 468 469 0.000 + . E . . +Sequence 470 480 0.000 + . . T . +Sequence 481 484 0.000 + . E . . +Sequence 485 490 0.000 + . . T . +Sequence 491 491 0.000 + . E . . +Sequence 492 496 0.000 + . . T . +Sequence 497 497 0.000 + . . . C +Sequence 498 500 0.000 + . . T . +Sequence 501 504 0.000 + . E . . +Sequence 505 510 0.000 + . . T . +Sequence 511 514 0.000 + . E . . +Sequence 515 517 0.000 + . . . C +Sequence 518 520 0.000 + . E . . +Sequence 521 532 0.000 + . . . C +Sequence 533 534 0.000 + . E . . +Sequence 535 547 0.000 + H . . . +Sequence 548 549 0.000 + . E . . +Sequence 550 554 0.000 + . . T . +Sequence 555 555 0.000 + . . . C +Sequence 556 561 0.000 + H . . . |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_geecee_out.geecee --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_geecee_out.geecee Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,2 @@ +#Sequence GC content +Sequence 0.36 |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_getorf_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_getorf_out.fasta Wed Mar 21 16:30:01 2012 -0400 |
| [ |
| @@ -0,0 +1,65 @@ +>Sequence_1 [1 - 51] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +VRCLKYLLLSLHRPQFS +>Sequence_2 [14 - 94] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +NTFFCPYTDHSFPNGFTPTRNSCASTN +>Sequence_3 [94 - 129] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +LKAVGLECYRFV +>Sequence_4 [133 - 231] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +LSASLALIKGSFSLLWKTLWKNTTSTSLSPLVC +>Sequence_5 [155 - 250] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +SKVHFLYFGRRCGRIQQVRVSPPWFADYWIQL +>Sequence_6 [3 - 272] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +SMPKIPSFVPTQTTVFLMALHRLEILVQALIESGWPRVLPVCIAERVSCPDQRFIFSTLE +DVVEEYNKYESLPPGLLITGYSCNTLRNTA +>Sequence_7 [235 - 309] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +LLDTVVIPFATPRNYLYELFSLYYM +>Sequence_8 [288 - 335] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +IIFPLLYVVGSSLIFL +>Sequence_9 [339 - 377] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +QVFYCFRPQCSCS +>Sequence_10 [254 - 391] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +YPSQHRVTIYMNYFPFIICSRFVFNLPLASLLLFSTSMFMFLGCFG +>Sequence_11 [395 - 427] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +YAVSLIFVVSS +>Sequence_12 [328 - 447] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +SSFSKSFTVFDLNVHVLRLFWIICGQFNLRCFFLKYLFMV +>Sequence_13 [411 - 521] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +SSLFLLKIFIHGLIFGLYLFRGQFIIYSVCIQQFFYF +>Sequence_14 [431 - 526] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +NIYSWFNFWFVLVQGPVHYLLCLYTAVLLFLV +>Sequence_15 [451 - 537] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +FLVCTCSGASSLFTLFVYSSSFIFSMILI +>Sequence_16 [531 - 487] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +NHTKNKRTAVYKQSK +>Sequence_17 [536 - 450] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +IKIILKIKELLYTNRVNNELAPEQVQTKN +>Sequence_18 [487 - 443] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +IMNWPLNKYKPKIKP +>Sequence_19 [468 - 439] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +TSTNQKLNHE +>Sequence_20 [439 - 410] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +INILRRNNED +>Sequence_21 [446 - 405] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +TMNKYFKKKQRRLN +>Sequence_22 [401 - 372] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +PHIIQNNLRT +>Sequence_23 [368 - 327] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +TLRSKTVKDLLKED +>Sequence_24 [426 - 292] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +EETTKIKLTAYYPKQPKNMNIEVENSKRLAKGRLKTNLLHIIKGK +>Sequence_25 [279 - 238] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +IVTRCCEGYYNCIQ +>Sequence_26 [234 - 175] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +SANQGGETRTCCILPQRLPK +>Sequence_27 [334 - 158] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +RKIKDEPTTYNKGKIIHIDSYAVLRRVLQLYPVISKPGGRDSYLLYSSTTSSKVEKMNL +>Sequence_28 [275 - 120] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +LRGVAKGITTVSSNQQTRGERLVLVVFFHNVFQSRENEPLIRARDALSYTNR +>Sequence_29 [162 - 112] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +TFDQGKRRAQLYKPVTL +>Sequence_30 [108 - 34] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +ANRFQLVLAQEFLVGVKPLGKLWSV +>Sequence_31 [50 - 3] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +ENCGLCRDKRRYFRHR +>Sequence_32 [154 - 2] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +SGQETRSAIQTGNTLGQPLSISACTRISSRCKAIRKTVVCVGTKEGILGIE |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_helixturnhelix_out.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_helixturnhelix_out.tabular Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,1 @@ +SeqName Start End Score Strand Maximum_score_at Standard_deviations |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_hmoment_out.hmoment --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_hmoment_out.hmoment Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,556 @@ +HMOMENT of Sequence from 1 to 561 + +Window: 10 Angle: 100 Max uH: 0.205 +Position uH +1 0.100 +2 0.071 +3 0.127 +4 0.152 +5 0.127 +6 0.056 +7 0.049 +8 0.032 +9 0.066 +10 0.041 +11 0.019 +12 0.020 +13 0.081 +14 0.125 +15 0.092 +16 0.044 +17 0.040 +18 0.051 +19 0.063 +20 0.038 +21 0.063 +22 0.052 +23 0.065 +24 0.086 +25 0.106 +26 0.073 +27 0.048 +28 0.088 +29 0.082 +30 0.044 +31 0.007 +32 0.035 +33 0.041 +34 0.094 +35 0.035 +36 0.045 +37 0.073 +38 0.069 +39 0.024 +40 0.055 +41 0.040 +42 0.007 +43 0.066 +44 0.009 +45 0.071 +46 0.111 +47 0.095 +48 0.144 +49 0.138 +50 0.143 +51 0.113 +52 0.120 +53 0.078 +54 0.051 +55 0.042 +56 0.035 +57 0.055 +58 0.027 +59 0.037 +60 0.029 +61 0.032 +62 0.077 +63 0.148 +64 0.108 +65 0.035 +66 0.098 +67 0.128 +68 0.118 +69 0.083 +70 0.108 +71 0.112 +72 0.076 +73 0.116 +74 0.102 +75 0.043 +76 0.090 +77 0.073 +78 0.025 +79 0.031 +80 0.058 +81 0.043 +82 0.066 +83 0.075 +84 0.146 +85 0.173 +86 0.140 +87 0.142 +88 0.200 +89 0.154 +90 0.089 +91 0.140 +92 0.121 +93 0.063 +94 0.055 +95 0.051 +96 0.057 +97 0.075 +98 0.136 +99 0.132 +100 0.068 +101 0.067 +102 0.076 +103 0.055 +104 0.019 +105 0.043 +106 0.041 +107 0.022 +108 0.064 +109 0.060 +110 0.085 +111 0.090 +112 0.111 +113 0.049 +114 0.083 +115 0.131 +116 0.137 +117 0.099 +118 0.119 +119 0.120 +120 0.054 +121 0.064 +122 0.059 +123 0.042 +124 0.026 +125 0.032 +126 0.078 +127 0.104 +128 0.117 +129 0.096 +130 0.116 +131 0.108 +132 0.084 +133 0.056 +134 0.063 +135 0.058 +136 0.050 +137 0.048 +138 0.025 +139 0.047 +140 0.093 +141 0.072 +142 0.027 +143 0.021 +144 0.053 +145 0.022 +146 0.049 +147 0.040 +148 0.103 +149 0.154 +150 0.105 +151 0.076 +152 0.127 +153 0.126 +154 0.105 +155 0.088 +156 0.107 +157 0.131 +158 0.095 +159 0.052 +160 0.114 +161 0.088 +162 0.041 +163 0.071 +164 0.067 +165 0.008 +166 0.056 +167 0.060 +168 0.064 +169 0.059 +170 0.055 +171 0.046 +172 0.030 +173 0.092 +174 0.062 +175 0.036 +176 0.019 +177 0.038 +178 0.032 +179 0.037 +180 0.051 +181 0.100 +182 0.051 +183 0.036 +184 0.088 +185 0.090 +186 0.039 +187 0.080 +188 0.076 +189 0.079 +190 0.061 +191 0.074 +192 0.090 +193 0.042 +194 0.024 +195 0.063 +196 0.065 +197 0.050 +198 0.061 +199 0.077 +200 0.136 +201 0.116 +202 0.037 +203 0.092 +204 0.120 +205 0.066 +206 0.026 +207 0.070 +208 0.075 +209 0.041 +210 0.075 +211 0.082 +212 0.034 +213 0.031 +214 0.023 +215 0.048 +216 0.047 +217 0.098 +218 0.098 +219 0.083 +220 0.059 +221 0.103 +222 0.099 +223 0.085 +224 0.110 +225 0.127 +226 0.163 +227 0.132 +228 0.190 +229 0.194 +230 0.197 +231 0.154 +232 0.205 +233 0.171 +234 0.166 +235 0.148 +236 0.161 +237 0.106 +238 0.035 +239 0.026 +240 0.026 +241 0.038 +242 0.084 +243 0.016 +244 0.060 +245 0.121 +246 0.061 +247 0.028 +248 0.076 +249 0.046 +250 0.050 +251 0.072 +252 0.042 +253 0.033 +254 0.083 +255 0.031 +256 0.093 +257 0.106 +258 0.042 +259 0.055 +260 0.053 +261 0.008 +262 0.030 +263 0.062 +264 0.078 +265 0.037 +266 0.114 +267 0.108 +268 0.078 +269 0.107 +270 0.134 +271 0.117 +272 0.091 +273 0.150 +274 0.147 +275 0.071 +276 0.025 +277 0.064 +278 0.022 +279 0.069 +280 0.072 +281 0.044 +282 0.107 +283 0.170 +284 0.176 +285 0.116 +286 0.110 +287 0.128 +288 0.078 +289 0.059 +290 0.055 +291 0.061 +292 0.020 +293 0.051 +294 0.048 +295 0.055 +296 0.112 +297 0.139 +298 0.083 +299 0.055 +300 0.105 +301 0.100 +302 0.049 +303 0.087 +304 0.086 +305 0.069 +306 0.131 +307 0.096 +308 0.090 +309 0.095 +310 0.134 +311 0.102 +312 0.098 +313 0.062 +314 0.055 +315 0.111 +316 0.098 +317 0.106 +318 0.131 +319 0.132 +320 0.098 +321 0.097 +322 0.096 +323 0.059 +324 0.089 +325 0.083 +326 0.088 +327 0.025 +328 0.103 +329 0.065 +330 0.028 +331 0.086 +332 0.109 +333 0.100 +334 0.094 +335 0.116 +336 0.109 +337 0.111 +338 0.063 +339 0.043 +340 0.074 +341 0.099 +342 0.090 +343 0.073 +344 0.067 +345 0.086 +346 0.092 +347 0.089 +348 0.092 +349 0.044 +350 0.045 +351 0.066 +352 0.039 +353 0.019 +354 0.013 +355 0.059 +356 0.069 +357 0.070 +358 0.045 +359 0.079 +360 0.117 +361 0.081 +362 0.138 +363 0.135 +364 0.083 +365 0.034 +366 0.096 +367 0.071 +368 0.034 +369 0.029 +370 0.038 +371 0.083 +372 0.105 +373 0.112 +374 0.070 +375 0.096 +376 0.096 +377 0.079 +378 0.078 +379 0.072 +380 0.088 +381 0.036 +382 0.059 +383 0.056 +384 0.043 +385 0.114 +386 0.114 +387 0.107 +388 0.101 +389 0.089 +390 0.079 +391 0.029 +392 0.098 +393 0.100 +394 0.036 +395 0.106 +396 0.075 +397 0.085 +398 0.090 +399 0.091 +400 0.096 +401 0.048 +402 0.032 +403 0.049 +404 0.070 +405 0.110 +406 0.059 +407 0.107 +408 0.102 +409 0.106 +410 0.081 +411 0.138 +412 0.143 +413 0.112 +414 0.138 +415 0.136 +416 0.127 +417 0.113 +418 0.107 +419 0.111 +420 0.092 +421 0.134 +422 0.098 +423 0.055 +424 0.044 +425 0.055 +426 0.056 +427 0.040 +428 0.041 +429 0.095 +430 0.158 +431 0.153 +432 0.106 +433 0.186 +434 0.187 +435 0.118 +436 0.167 +437 0.162 +438 0.168 +439 0.108 +440 0.155 +441 0.121 +442 0.121 +443 0.059 +444 0.053 +445 0.098 +446 0.087 +447 0.119 +448 0.149 +449 0.149 +450 0.113 +451 0.069 +452 0.083 +453 0.084 +454 0.095 +455 0.119 +456 0.117 +457 0.100 +458 0.102 +459 0.096 +460 0.100 +461 0.116 +462 0.187 +463 0.150 +464 0.080 +465 0.106 +466 0.115 +467 0.085 +468 0.036 +469 0.098 +470 0.095 +471 0.112 +472 0.061 +473 0.077 +474 0.119 +475 0.141 +476 0.099 +477 0.154 +478 0.184 +479 0.185 +480 0.136 +481 0.194 +482 0.178 +483 0.177 +484 0.138 +485 0.132 +486 0.087 +487 0.055 +488 0.057 +489 0.051 +490 0.037 +491 0.087 +492 0.035 +493 0.031 +494 0.080 +495 0.053 +496 0.023 +497 0.045 +498 0.033 +499 0.030 +500 0.087 +501 0.089 +502 0.035 +503 0.064 +504 0.125 +505 0.132 +506 0.069 +507 0.085 +508 0.072 +509 0.088 +510 0.050 +511 0.049 +512 0.043 +513 0.064 +514 0.071 +515 0.111 +516 0.109 +517 0.082 +518 0.089 +519 0.054 +520 0.038 +521 0.032 +522 0.032 +523 0.038 +524 0.054 +525 0.059 +526 0.015 +527 0.068 +528 0.073 +529 0.026 +530 0.106 +531 0.055 +532 0.047 +533 0.103 +534 0.091 +535 0.049 +536 0.031 +537 0.032 +538 0.038 +539 0.068 +540 0.130 +541 0.077 +542 0.043 +543 0.104 +544 0.058 +545 0.045 +546 0.108 +547 0.084 +548 0.139 +549 0.189 +550 0.130 +551 0.062 +552 0.136 |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_iep_out.iep --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_iep_out.iep Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,31 @@ +IEP of Sequence from 1 to 561 +Isoelectric Point = 5.0278 + + pH Bound Charge + 1.00 108.00 1.00 + 1.50 107.99 0.99 + 2.00 107.98 0.98 + 2.50 107.93 0.93 + 3.00 107.80 0.80 + 3.50 107.56 0.56 + 4.00 107.28 0.28 + 4.50 107.10 0.10 + 5.00 107.00 0.00 + 5.50 106.91 -0.09 + 6.00 106.67 -0.33 + 6.50 105.94 -1.06 + 7.00 103.73 -3.27 + 7.50 97.29 -9.71 + 8.00 81.33 -25.67 + 8.50 53.56 -53.44 + 9.00 25.75 -81.25 + 9.50 9.75 -97.25 + 10.00 3.29 -103.71 + 10.50 1.06 -105.94 + 11.00 0.34 -106.66 + 11.50 0.11 -106.89 + 12.00 0.03 -106.97 + 12.50 0.01 -106.99 + 13.00 0.00 -107.00 + 13.50 0.00 -107.00 + 14.00 0.00 -107.00 |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_isochore_out.isochore --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_isochore_out.isochore Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,7 @@ +Position Percent G+C 1 .. 561 +140 0.446 +196 0.414 +252 0.396 +308 0.357 +364 0.332 +420 0.282 |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_marscan_out.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_marscan_out.tabular Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,4 @@ +SeqName Start End Score Strand type start8bp end8bp start16bp end16bp +hg17 440 492 0.000 + MAR/SAR recognition site (MRS) 440 447 477 492 +hg17 13640 13750 0.000 + MAR/SAR recognition site (MRS) 13640 13647 13735 13750 +hg17 15229 15392 0.000 + MAR/SAR recognition site (MRS) 15385 15392 15229 15244 |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_maskfeat_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_maskfeat_out.fasta Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,11 @@ +>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt +tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac +cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg +aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg +gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt +tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac +ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt +ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt +tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa +aacaattctaatggtcaaaaa |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_maskseq_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_maskseq_out.fasta Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,11 @@ +>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +NNNcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt +tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac +cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg +aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg +gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt +tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac +ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt +ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt +tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa +aacaattctaatggtcaaaaa |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_matcher_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_matcher_out.fasta Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,6 @@ +>Sequence +CTTTAGCAAGTCTTTTACTGTTTTCGACCTCAATGTTCATGTTCTTAGGTTGTTTTGGAT +A +>hg17 +CTTCAGCAAGTTCCTTACTGTCTTTAAGCCTTGTTTTCATCATCT--GGATAATGGGGAT +A |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_msbar_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_msbar_out.fasta Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,11 @@ +>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt +tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac +cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg +aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg +gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt +tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac +ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt +ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt +tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa +aacaattctaatggtcaaaaa |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_needle_out.score --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_needle_out.score Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,4 @@ +Sequence hg17 20190 (604.5) + +#--------------------------------------- +#--------------------------------------- |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_newcpgreport_out.newcpgreport --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_newcpgreport_out.newcpgreport Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,11 @@ +ID Sequence 561 BP. +XX +DE CpG Island report. +XX +CC Obs/Exp ratio > 0.60. +CC % C + % G > 50.00. +CC Length > 200. +XX +FH Key Location/Qualifiers +FT no islands detected +// |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_newcpgseek_out.newcpgseek --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_newcpgseek_out.newcpgseek Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,9 @@ + + +NEWCPGSEEK of Sequence from 1 to 561 +with score > 17 + + Begin End Score CpG %CG CG/GC + 121 141 34 3 57.1 1.00 + 261 272 43 3 75.0 1.00 +------------------------------------------- \ No newline at end of file |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_newseq_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_newseq_out.fasta Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>cytoc fragment of cytochrome c +KKKEERADLIAY |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_noreturn_out.noreturn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_noreturn_out.noreturn Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,11 @@ +>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +gttcgatgcc taaaatacct tcttttgtcc ctacacagac cacagttttc ctaatggctt +tacaccgact agaaattctt gtgcaagcac taattgaaag cggttggcct agagtgttac +cggtttgtat agctgagcgc gtctcttgcc ctgatcaaag gttcattttc tctactttgg +aagacgttgt ggaagaatac aacaagtacg agtctctccc ccctggtttg ctgattactg +gatacagttg taataccctt cgcaacaccg cgtaactatc tatatgaatt attttccctt +tattatatgt agtaggttcg tctttaatct tcctttagca agtcttttac tgttttcgac +ctcaatgttc atgttcttag gttgttttgg ataatatgcg gtcagtttaa tcttcgttgt +ttcttcttaa aatatttatt catggtttaa tttttggttt gtacttgttc aggggccagt +tcattattta ctctgtttgt atacagcagt tcttttattt ttagtatgat tttaatttaa +aacaattcta atggtcaaaa a |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_notseq_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_notseq_out.fasta Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,11 @@ +>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt +tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac +cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg +aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg +gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt +tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac +ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt +ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt +tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa +aacaattctaatggtcaaaaa |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_nthseq_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_nthseq_out.fasta Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,11 @@ +>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt +tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac +cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg +aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg +gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt +tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac +ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt +ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt +tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa +aacaattctaatggtcaaaaa |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_palindrome_out.palindrome --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_palindrome_out.palindrome Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,15 @@ +Palindromes of: Sequence +Sequence length is: 561 +Start at position: 1 +End at position: 561 +Minimum length of Palindromes is: 10 +Maximum length of Palindromes is: 100 +Maximum gap between elements is: 100 +Number of mismatches allowed in Palindrome: 0 + + + +Palindromes: + + + |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_pasteseq_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_pasteseq_out.fasta Wed Mar 21 16:30:01 2012 -0400 |
| b |
| b'@@ -0,0 +1,371 @@\n+>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;\n+gtttgccatcttttgctgctctagggaatccagcagctgtcaccatgtaaacaagcccag\n+gctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagt\n+caggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagcca\n+ctaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTG\n+ACTGGAGGAAGAGATGCTATAAAGACCACCTTTTAAAACTTCCC----------------\n+---------------AAATACT-GCCACTGATGTCCTG-----ATGGAGGTA-------T\n+GAA-------------------AACATCCACTAAAATTTGTGGTTTATTCATTTTTCATT\n+ATTTTGTTTAAGGAGGTCTATAGTGGAAGAGGGAGATATTTGGggaaatt---ttgtata\n+gactagctttcacgatgttagggaattattattgtgtgataatggtcttgcagttaca-c\n+agaaattcttccttattttttgggaa---gcaccaaag----tagggat---aaaatgtc\n+atgatgtgtgcaatacactttaaaatgtttttg-----ccaaaataatt-----------\n+-----aatgaagc--aaatatggaaa-ataataattattaaatctaggtgatgggtatat\n+tgtagttcactatagtattgcacacttttctgtatgtttaaatttttcatttaaaaaaaa\n+actttgagc-----tagacaccaggctatgagctaggagcatagcaatgaccaa------\n+------------------------------------------------------------\n+----------------------------atagactcctaccaa-----------------\n+---------------------------------ctc-aaagaatgcacattctCTGGGAA\n+ACATGTTTCCATTAGGAAGCCTCGAATGCAATGTGACTGTGGTCTCCAGGACCTG-TGTG\n+ATCCTGGCTTTTCCTGTTCCCTCCG---CATCATCACTGCAGGTGTGTTTTCCCAAGTTT\n+TAAACATTTA------CCTTCCCAGTGGCCTTGCGTCTAGAGGAATCCCTGTATAGTGGT\n+-ACATGAATATAACACATAACAAA-AATCATCTCTATGGTGTGTGTTGTTCCTGGGGTTC\n+Aattcagcaaattttccctg-ggcacccatgtgttcttggcactggaaaagtaccgggac\n+tgaaacagttgatggccca-atccctgtcctct---taaaacctaagggaggagaTGGAA\n+AGGGG-CACCCAACCCAGACTGAGAGACAGGAATTAGCTGCAAGGGGAACTAGGAAAAGC\n+TTCTTTA---AGGATGGAGAGGCCCTAGTGGAAT-GGGGAGATTCTTCCGGGAGAAGCGA\n+TGGATGCACAGTTGGGCATCCCCACAGACGGACTGGAAAGAAAAAAGGCCTGGAGGAATC\n+AATGTG-------CAATGTATGTGTGTTCCCTGGTTcaagggctgg-gaactttctcta-\n+aagggccaggtagaaaacattttaggctttctaagccaag--gcaaaat-tgaggatatt\n+acatgggtacttatacaacaagaataaacaatt---tacacaattttttgttgacagaat\n+tcaaaactttat----agacacagaaatgcaaatttcctgtaattttcccat-gagaact\n+attcttct--tttgttttgttttgcgacAGGGTTGCGCtgatcctcccgcctcagtctcc\n+ctaagtgctgagatgttgcaggaagtcagggaccccgaacagagagatcggctggagccg\n+tggcagaggaacataaattttgaagatttcattttaatatggacacttatcagttcccaa\n+ataatacttttataattttttatgcctgtctttgctttaatctcttaatcctgttatctt\n+cataagctaaggatgtacgtcacctcaggaccactgtgataattgtgttaactgtacaga\n+ttgattgcaaaacatgtgtgtttgaacaatatgaaatcagtgcaccttgaaaaagagcag\n+aataacagcaatttttagggaacaagggaagacaactataaggtctgactgcctgcgggg\n+tcgggcaaagggagccatatttttcttcttgcagagagcctataaatagacctgcaagta\n+ggagagatattgctaatttcttttgctagcatggaatattaatattaacaccctgggaaa\n+ggaatgcattcctggggggaggtctataaatggccgctctgggaatgtctatcctacgca\n+atggagataaggactgagatacgccctggtctcctgcagtaccctcaggcttactagggt\n+ggtgaaaaactccgccctggtaaatttgtggtcagaccagttttctgctctcgaacactg\n+ttttctgttgtttaagatgtttatcaagacaatacgtgcaccgctgaacacagaccctta\n+tcagtagttctcctttttgccctttgaagcatgtgatctactccctgttttacaccccct\n+caccttttgaaacccttaataaaaaacttgctggttt-gaggctcaggtgggcatcacag\n+tactaccgatatgtgatgtcacccccggcggcccagctgtaaaattcctctctttgtact\n+ctctctctttatttctcagccagctgacacttatggaaaatagaaagaacctacgttgaa\n+atattgggggcaggttcccccaataTCTGGTGCCCAACGTGGGAtactgagattacaagc\n+atgagccactgcatctggcctcttcttttgatttttttttttcaaacttttacaaatgta\n+gaaaccattcttagcttttgggcattaccaaacccggcagtgg-caggctcggttcacca\n+acgtcatttgcagttccccgCTTTATGTTATGGgttttgttttgttttgtttttttt-at\n+tgagacagagtttcactcttgttgcccaggctgtagtgcaatggtctgatcttggctcac\n+tgcaacctccacttcccaggttcaagccattctcctgcctcagcctctcaagtagctggg\n+attacagacactcaccaccacacctggctaattttgtatttttagtagagatgaggtttc\n+accatgttggccaggctggtctcgaaatcctgacctcaggtgatccacccaccttggcct\n+cccaaagtgctgggattacaggcttgagctaccacgcctggctGGGTTGGTTCTCAATGG\n+AGTGGTTTGTTTTTGGAGCTGCTCT-GCGCAGtggggaccagaataggcctg--------\n+-----------ggttcctagcccattgctattcctt----accagctgtggattctaagg\n+aaagtcatttaacctcgctggaccttag-attcctcatccctgaaGCCCAAGGGTaaaac\n+aaaacaaaacaaaacaaaacaaaccaaCCCATCATGTAAAGCGGGGAACTACAAACGATA\n+CAGGTGAAACATGCCTACCACACCACTCACAGGCT--ATGATGACAAAAACGTGGCTACA\n+TCTGGGACCACCCCCCAACCCCCACTTTGTACGTAGGAAATACGGAGTTGAGGATGGAGA\n+CCCACAGTATGTCCAGAGTGTCCCCAAAGGCCACAGTGCCCGCCTGGAGCCCTCCAGAGA\n+GCGTGCACTCCCTGGGGTG'..b'GAGGCCATGTAGAGAAAGGAATGACCTAGGAAAGTTGGCCTGGAAGTGGAG\n+GGAAGGATGGTGTGGGAAAAGCAGGAA--------TCTCGGAGACCAGCTTAGAGGCTTG\n+GCAGTCACCTGGGTGCAGG-ATACAAGGGCCTGAGCCAAAGTGGTGAGGGAGGGTGGAAG\n+GAGGCAGCCCAGAGAATGACCCTCCATGCCCACGGGGAAGGCAGAGGGCTCT-GAGAGCG\n+A--TTCCTCCCACATG-CT-GAGCACTTGTTCTCCCTCTTCCTCCTGCATAGCAGTCAGT\n+CTCCTCCAAACAGAAAGTCACCGGTTTGGACTTCATTCCTGGGCTCCACCCCATCCTGAC\n+CTTATCCAAGATGGACCAGACACTGGCAGTCTACCAACAGATCCTCACCAGTATGCCTTC\n+CAGAAACGTGATCCAAATATCCAACGACCTGGAGAACCTCCGGGATCTTCTTCACGTGCT\n+GGCCTTCTCTAAGAGCTGCCACTTGCCCTGGGCCAGTGGCCTGGAGACCTTGGACAGCCT\n+GGGGGGTGTCCTGGAAGCTTCAGGCTACTCCACAGAGGTGGTGGCCCTGAGCAGGCTGCA\n+GGGGTCTCTGCAGGACATGCTGTGGCAGCTGGACCTCAGCCCTGGGTGCTGAGGCCTTGA\n+AGGTCACTCTTCCTGCAAGGACTACGTTAAGGGAAGGAACTCTGGCTTCCAGGTATCTCC\n+AGGATTGAAGAGCATTGCATGGACACCCCTTATCCAGGACTCTGTCAATT--TCCCTGAC\n+TCCTCTAAGCCACTCTTCCAAAGGCATAAGACCCTAAGCCTCCTTTTGCTTGAAACCAAA\n+GATATATACACAGGATCCTATTCTCACCAGGAAGGGGG-TCCACCC-AGCAAAGAGTGGG\n+CTGCATCTGGGATTCCCACCAAGGTCTTCAGCCATCA---ACAAGAGTTGTCTTGTCCCC\n+TCT-TGACCCATCT-----------------CCCCCTCACTGAATGCCTCAATGTGACCA\n+GGGGTGATTTCAGAGAGGGCAGAGGGGTAGGCAGAGCCTTTGGATGACCA--GAACAAGG\n+TTCCCTCTGAGAATTCCAAGGAGTTCCATGAAGACCACATCCACACACG--CAGGAACTC\n+CC--AGCAACACAAGCTGGAA---GCACATGTTTATTTATTCTGCATTTTATTCTGGATG\n+GATTTGAAGCAAAGCACCAGCTTCTCCAGGCTCTTTGGGGTCAGCCAGGGCCAGGGGTCT\n+CCCTGGAGTGCAGTTTCCAATCCCATAGATGGGTC-TGGCTGAGCTGAACCCA---TTTT\n+GAGTGACT----CGAGGGTTGGG-TTCATCTGAGCAAGAGCTGGCAAAGGTGGCTCTCCA\n+GTTAGTTCTCTCGTAACTGGTTTCATTTCTACTGTGACTGATGTTACATCACAGTGTTTG\n+CAATGGTGTTGCCCTGAGTGGATCTCCAAGGACCAGGTTATTTTAAAA---AGATTTGTT\n+TTGTCAAGTGTCATATGTAGGTGTCTGCACCCAGGGGTGGG-GAATGTTTGGGCAGAAGG\n+GAGAAGGATCTAGAATGTGTTTTCTGAATAACATTTGTGTGGTGGGTTCTTTGGAAGGAG\n+TGAGA-TCATTTTCTTATCTTCTGCAATTGCTTAGGATGTTTTTCATGAAAA--------\n+----TAGCTCTTTCAG-GGGGGTTGTGAGGCCTGGCCAGGCACCCCCTGGAGAGAAGTTT\n+CTGGCCCTGGCTGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCA\n+GAATAAAACGCAAAGGGCTGAAAGCCATTTGTTGGGGCAGTGGTAAGCTCTGGCTTTCTC\n+CGACTGCTAGGGAGTGGTCTTTCCTATCATGGAGTGACGGTCCCACACTGGTGACTGCGA\n+TCTTCAGAGCAGGGGTCCTTGGTGT-GACCCTCTGAATGGTCCAGGGTTGATCACACTCT\n+GGGTTTATTACATGGCAG-----TGTTCCTATTTGGGGCTTGCATGCCAAATTGTAGTTC\n+TTGTCTGATTGGCTCACCC-AAGCAAGGCCAAAATTACCAAAAATCTTGGGGGG--TTTT\n+TACTC-CAGTGGTGAAGAAAACTCCTTTAGCAGG-TGGTCCTGAGACCT-GACAAGCACT\n+GCTAGGCGAGTGCCAGGACTCCCCAGGCCAGGCCACCAGGATGGCCCTTCCCACTGGAGG\n+TCACATTCAGGAAGATGAAAGAGGAGGTTTGGGGTCTGCCACCATCCTGCTGCTGTGTTT\n+TTGCTATCACACAGTGGGTGGTGGATCTGTCCAAGGAAACTTGAATCAAAGCAGTTAAC-\n+TTTAAGactgagcacctgcttcatgctcagccctgactggtgctataggctggagaagct\n+cacccaataaacattaagatt-gaggcctgccctcagggatcttgcattcccagtggTCA\n+AACC-GCACTCACCCATGTGCCAAGGTGGGGTA-TTTACCACAGCAG--CTGAACAGCCA\n+AATGCATGGTGCAGTTGACAGCAGGTGGGAAATGGTATGAGCTGAGGGGGGCCGTGCCCA\n+GGGGCCCACAGG-GAACCCTGCTTGCACTTTGTAACATGTTTA-----CTTTTCagggca\n+tcttagctt---ctatta-----tagccacatccctttga---aacaagataactgagaa\n+tttaaaaataagaa-----aata--TGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGC\n+TTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGC\n+TTCAAATCCATCCAGAATAAAACGCAGATGCTTTGCTTCAAATCCATCCAGAATAAAACG\n+CAAATGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAA\n+ACGCATGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAA\n+AACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAA\n+AACGCAGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGA\n+GAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGA\n+GAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGA\n+GAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGATGCTTTGCTTCAAATC\n+CATCCAGAATAAAACGCAgttcgatgcctaaaataccttcttttgtccctacacagacca\n+cagttttcctaatggctttacaccgactagaaattcttgtgcaagcactaattgaaagcg\n+gttggcctagagtgttaccggtttgtatagctgagcgcgtctcttgccctgatcaaaggt\n+tcattttctctactttggaagacgttgtggaagaatacaacaagtacgagtctctccccc\n+ctggtttgctgattactggatacagttgtaatacccttcgcaacaccgcgtaactatcta\n+tatgaattattttccctttattatatgtagtaggttcgtctttaatcttcctttagcaag\n+tcttttactgttttcgacctcaatgttcatgttcttaggttgttttggataatatgcggt\n+cagtttaatcttcgttgtttcttcttaaaatatttattcatggtttaatttttggtttgt\n+acttgttcaggggccagttcattatttactctgtttgtatacagcagttcttttattttt\n+agtatgattttaatttaaaacaattctaatggtcaaaaa\n' |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_patmatdb_out.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_patmatdb_out.tabular Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,41 @@ +SeqName Start End Score Strand +Sequence 560 561 2 + +Sequence 559 560 2 + +Sequence 558 559 2 + +Sequence 557 558 2 + +Sequence 550 551 2 + +Sequence 544 545 2 + +Sequence 541 542 2 + +Sequence 540 541 2 + +Sequence 539 540 2 + +Sequence 534 535 2 + +Sequence 449 450 2 + +Sequence 431 432 2 + +Sequence 430 431 2 + +Sequence 429 430 2 + +Sequence 409 410 2 + +Sequence 393 394 2 + +Sequence 364 365 2 + +Sequence 340 341 2 + +Sequence 326 327 2 + +Sequence 287 288 2 + +Sequence 274 275 2 + +Sequence 264 265 2 + +Sequence 252 253 2 + +Sequence 204 205 2 + +Sequence 201 202 2 + +Sequence 196 197 2 + +Sequence 193 194 2 + +Sequence 181 182 2 + +Sequence 158 159 2 + +Sequence 157 158 2 + +Sequence 98 99 2 + +Sequence 97 98 2 + +Sequence 92 93 2 + +Sequence 85 86 2 + +Sequence 74 75 2 + +Sequence 73 74 2 + +Sequence 53 54 2 + +Sequence 14 15 2 + +Sequence 13 14 2 + +Sequence 12 13 2 + |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_pepcoil_out.pepcoil --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_pepcoil_out.pepcoil Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,6 @@ +PEPCOIL of Sequence + using a window of 28 residues + + +Other structures from 1 to 561 (561 residues) + Max score: 0.827 (probability 0.00) |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_pepstats_out.pepstats --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_pepstats_out.pepstats Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,48 @@ +PEPSTATS of Sequence from 1 to 561 + +Molecular weight = 48582.66 Residues = 561 +Average Residue Weight = 86.600 Charge = 0.0 +Isoelectric Point = 5.0278 +A280 Molar Extinction Coefficient = 0 +A280 Extinction Coefficient 1mg/ml = 0.00 +Improbability of expression in inclusion bodies = 0.520 + +Residue Number Mole% DayhoffStat +A = Ala 135 24.064 2.798 +B = Asx 0 0.000 0.000 +C = Cys 106 18.895 6.515 +D = Asp 0 0.000 0.000 +E = Glu 0 0.000 0.000 +F = Phe 0 0.000 0.000 +G = Gly 98 17.469 2.080 +H = His 0 0.000 0.000 +I = Ile 0 0.000 0.000 +J = --- 0 0.000 0.000 +K = Lys 0 0.000 0.000 +L = Leu 0 0.000 0.000 +M = Met 0 0.000 0.000 +N = Asn 0 0.000 0.000 +O = --- 0 0.000 0.000 +P = Pro 0 0.000 0.000 +Q = Gln 0 0.000 0.000 +R = Arg 0 0.000 0.000 +S = Ser 0 0.000 0.000 +T = Thr 222 39.572 6.487 +U = --- 0 0.000 0.000 +V = Val 0 0.000 0.000 +W = Trp 0 0.000 0.000 +X = Xaa 0 0.000 0.000 +Y = Tyr 0 0.000 0.000 +Z = Glx 0 0.000 0.000 + +Property Residues Number Mole% +Tiny (A+C+G+S+T) 561 100.000 +Small (A+B+C+D+G+N+P+S+T+V) 561 100.000 +Aliphatic (A+I+L+V) 135 24.064 +Aromatic (F+H+W+Y) 0 0.000 +Non-polar (A+C+F+G+I+L+M+P+V+W+Y) 339 60.428 +Polar (D+E+H+K+N+Q+R+S+T+Z) 222 39.572 +Charged (B+D+E+H+K+R+Z) 0 0.000 +Basic (H+K+R) 0 0.000 +Acidic (B+D+E+Z) 0 0.000 + |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_plotorf_out.png |
| b |
| Binary file test-data/emboss_plotorf_out.png has changed |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_plotorf_out1.png |
| b |
| Binary file test-data/emboss_plotorf_out1.png has changed |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_polydot_out.png |
| b |
| Binary file test-data/emboss_polydot_out.png has changed |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_prettyseq_out.prettyseq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_prettyseq_out.prettyseq Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,42 @@ +PRETTYSEQ of Sequence from 1 to 561 + + ---------|---------|---------|---------|---------|---------| + 1 gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt 60 + 1 V R C L K Y L L L S L H R P Q F S * W L 2 + + ---------|---------|---------|---------|---------|---------| + 61 tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac 120 + 3 Y T D * K F L C K H * L K A V G L E C Y 9 + + ---------|---------|---------|---------|---------|---------| + 121 cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg 180 + 10 R F V * L S A S L A L I K G S F S L L W 16 + + ---------|---------|---------|---------|---------|---------| + 181 aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg 240 + 17 K T L W K N T T S T S L S P L V C * L L 2 + + ---------|---------|---------|---------|---------|---------| + 241 gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt 300 + 3 D T V V I P F A T P R N Y L Y E L F S L 22 + + ---------|---------|---------|---------|---------|---------| + 301 tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac 360 + 23 Y Y M * * V R L * S S F S K S F T V F D 11 + + ---------|---------|---------|---------|---------|---------| + 361 ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt 420 + 12 L N V H V L R L F W I I C G Q F N L R C 31 + + ---------|---------|---------|---------|---------|---------| + 421 ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt 480 + 32 F F L K Y L F M V * F L V C T C S G A S 10 + + ---------|---------|---------|---------|---------|---------| + 481 tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa 540 + 11 S L F T L F V Y S S S F I F S M I L I * 29 + + ---------|---------|- + 541 aacaattctaatggtcaaaaa 561 + 1 N N S N G Q K 7 + |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_primersearch.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_primersearch.fasta Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,7 @@ +# This is my primer file +D1S243 cacacaggctcacatgcc gctccagcgtcatggact +D1S468 aattaaccgttttggtcct gcgacacacacttccc +D1S2845 ccaaagggtgcttctc gtggcattccaacctc +D1S1608 gatggcttttggggactatt cactgagccaagtgacacag +D1S2893 aaaacatcaactctcccctg ctcaaaccccaataagcctt +D1S2660 cacacatgcacatgcac agtgacaccagcaggg |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_primersearch_out.primersearch --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_primersearch_out.primersearch Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,12 @@ + +Primer name D1S243 + +Primer name D1S468 + +Primer name D1S2845 + +Primer name D1S1608 + +Primer name D1S2893 + +Primer name D1S2660 |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_revseq_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_revseq_out.fasta Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,11 @@ +>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +tttttgaccattagaattgttttaaattaaaatcatactaaaaataaaagaactgctgta +tacaaacagagtaaataatgaactggcccctgaacaagtacaaaccaaaaattaaaccat +gaataaatattttaagaagaaacaacgaagattaaactgaccgcatattatccaaaacaa +cctaagaacatgaacattgaggtcgaaaacagtaaaagacttgctaaaggaagattaaag +acgaacctactacatataataaagggaaaataattcatatagatagttacgcggtgttgc +gaagggtattacaactgtatccagtaatcagcaaaccaggggggagagactcgtacttgt +tgtattcttccacaacgtcttccaaagtagagaaaatgaacctttgatcagggcaagaga +cgcgctcagctatacaaaccggtaacactctaggccaaccgctttcaattagtgcttgca +caagaatttctagtcggtgtaaagccattaggaaaactgtggtctgtgtagggacaaaag +aaggtattttaggcatcgaac |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_seqmatchall_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_seqmatchall_out.fasta Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,3 @@ + +#--------------------------------------- +#--------------------------------------- |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_seqret_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_seqret_out.fasta Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,11 @@ +>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt +tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac +cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg +aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg +gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt +tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac +ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt +ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt +tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa +aacaattctaatggtcaaaaa |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_sigcleave_out.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_sigcleave_out.tabular Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,6 @@ +SeqName Start End Score Strand mature_peptide +Sequence 27 39 5.175 + CCACAGTTTTCCTAATGGCTTTACACCGACTAGAAATTCTTGTGCAAGCA +Sequence 253 265 4.809 + CACCGCGTAACTATCTATATGAATTATTTTCCCTTTATTATATGTAGTAG +Sequence 29 41 4.790 + ACAGTTTTCCTAATGGCTTTACACCGACTAGAAATTCTTGTGCAAGCACT +Sequence 541 553 3.820 + GTCAAAAA +Sequence 30 42 3.530 + CAGTTTTCCTAATGGCTTTACACCGACTAGAAATTCTTGTGCAAGCACTA |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_sirna_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_sirna_out.fasta Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,158 @@ +>Sequence_92 %GC 50.0 Score 9 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +aattgaaagcggttggcctagag +>Sequence_53 %GC 45.0 Score 8 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +aatggctttacaccgactagaaa +>Sequence_97 %GC 55.0 Score 8 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +aaagcggttggcctagagtgtta +>Sequence_98 %GC 55.0 Score 8 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +aagcggttggcctagagtgttac +>Sequence_201 %GC 55.0 Score 8 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +aacaagtacgagtctctcccccc +>Sequence_14 %GC 40.0 Score 7 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +aataccttcttttgtccctacac +>Sequence_85 %GC 40.0 Score 7 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +aagcactaattgaaagcggttgg +>Sequence_181 %GC 40.0 Score 7 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +aagacgttgtggaagaatacaac +>Sequence_196 %GC 40.0 Score 7 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +aatacaacaagtacgagtctctc +>Sequence_204 %GC 60.0 Score 7 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +aagtacgagtctctcccccctgg +>Sequence_252 %GC 60.0 Score 7 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +aatacccttcgcaacaccgcgta +>Sequence_264 %GC 40.0 Score 7 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +aacaccgcgtaactatctatatg +>Sequence_38 %GC 45.0 Score 6 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +gaccacagttttcctaatggctt +>Sequence_73 %GC 35.0 Score 6 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +aaattcttgtgcaagcactaatt +>Sequence_96 %GC 55.0 Score 6 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +gaaagcggttggcctagagtgtt +>Sequence_118 %GC 50.0 Score 6 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +taccggtttgtatagctgagcgc +>Sequence_200 %GC 50.0 Score 6 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +caacaagtacgagtctctccccc +>Sequence_326 %GC 35.0 Score 6 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +aatcttcctttagcaagtctttt +>Sequence_364 %GC 35.0 Score 6 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +aatgttcatgttcttaggttgtt +>Sequence_12 %GC 35.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +aaaataccttcttttgtccctac +>Sequence_13 %GC 35.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +aaataccttcttttgtccctaca +>Sequence_16 %GC 45.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +taccttcttttgtccctacacag +>Sequence_32 %GC 45.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +tacacagaccacagttttcctaa +>Sequence_52 %GC 45.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +taatggctttacaccgactagaa +>Sequence_74 %GC 35.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +aattcttgtgcaagcactaattg +>Sequence_88 %GC 45.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +cactaattgaaagcggttggcct +>Sequence_91 %GC 45.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +taattgaaagcggttggcctaga +>Sequence_128 %GC 55.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +tatagctgagcgcgtctcttgcc +>Sequence_173 %GC 45.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +tactttggaagacgttgtggaag +>Sequence_193 %GC 35.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +aagaatacaacaagtacgagtct +>Sequence_198 %GC 45.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +tacaacaagtacgagtctctccc +>Sequence_243 %GC 45.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +tacagttgtaatacccttcgcaa +>Sequence_251 %GC 55.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +taatacccttcgcaacaccgcgt +>Sequence_313 %GC 40.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +taggttcgtctttaatcttcctt +>Sequence_340 %GC 35.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +aagtcttttactgttttcgacct +>Sequence_393 %GC 35.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +aatatgcggtcagtttaatcttc +>Sequence_489 %GC 40.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +tactctgtttgtatacagcagtt +>Sequence_34 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +cacagaccacagttttcctaatg +>Sequence_36 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +cagaccacagttttcctaatggc +>Sequence_61 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +tacaccgactagaaattcttgtg +>Sequence_63 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +caccgactagaaattcttgtgca +>Sequence_70 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +tagaaattcttgtgcaagcacta +>Sequence_84 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +caagcactaattgaaagcggttg +>Sequence_110 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +tagagtgttaccggtttgtatag +>Sequence_112 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +gagtgttaccggtttgtatagct +>Sequence_135 %GC 60.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +gagcgcgtctcttgccctgatca +>Sequence_180 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +gaagacgttgtggaagaatacaa +>Sequence_183 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +gacgttgtggaagaatacaacaa +>Sequence_203 %GC 60.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +caagtacgagtctctcccccctg +>Sequence_210 %GC 60.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +gagtctctcccccctggtttgct +>Sequence_245 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +cagttgtaatacccttcgcaaca +>Sequence_254 %GC 60.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +tacccttcgcaacaccgcgtaac +>Sequence_263 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +caacaccgcgtaactatctatat +>Sequence_266 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +caccgcgtaactatctatatgaa +>Sequence_348 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +tactgttttcgacctcaatgttc +>Sequence_395 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +tatgcggtcagtttaatcttcgt +>Sequence_157 %GC 30.0 Score 3 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +aaaggttcattttctctactttg +>Sequence_158 %GC 30.0 Score 3 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +aaggttcattttctctactttgg +>Sequence_207 %GC 65.0 Score 3 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +tacgagtctctcccccctggttt +>Sequence_325 %GC 35.0 Score 3 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +taatcttcctttagcaagtcttt +>Sequence_392 %GC 35.0 Score 3 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +taatatgcggtcagtttaatctt +>Sequence_409 %GC 30.0 Score 3 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +aatcttcgttgtttcttcttaaa +>Sequence_11 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +taaaataccttcttttgtcccta +>Sequence_41 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +cacagttttcctaatggctttac +>Sequence_43 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +cagttttcctaatggctttacac +>Sequence_67 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +gactagaaattcttgtgcaagca +>Sequence_72 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +gaaattcttgtgcaagcactaat +>Sequence_130 %GC 65.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +tagctgagcgcgtctcttgccct +>Sequence_192 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +gaagaatacaacaagtacgagtc +>Sequence_195 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +gaatacaacaagtacgagtctct +>Sequence_236 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +tactggatacagttgtaataccc +>Sequence_241 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +gatacagttgtaatacccttcgc +>Sequence_304 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +tatatgtagtaggttcgtcttta +>Sequence_306 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +tatgtagtaggttcgtctttaat +>Sequence_310 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +tagtaggttcgtctttaatcttc +>Sequence_358 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +gacctcaatgttcatgttcttag +>Sequence_370 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +catgttcttaggttgttttggat +>Sequence_156 %GC 30.0 Score 1 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +caaaggttcattttctctacttt +>Sequence_403 %GC 30.0 Score 1 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +cagtttaatcttcgttgtttctt |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_sixpack_out2.sixpack --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_sixpack_out2.sixpack Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,134 @@ + + + V R C L K Y L L L S L H R P Q F S * W L F1 + F D A * N T F F C P Y T D H S F P N G F F2 + S M P K I P S F V P T Q T T V F L M A L F3 + gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt + 10 20 30 40 50 60 + ----:----|----:----|----:----|----:----|----:----|----:----| + caagctacggattttatggaagaaaacagggatgtgtctggtgtcaaaaggattaccgaa + T R H R F Y R R K D R C L G C N E * H S F6 + X E I G L I G E K T G V C V V T K R I A F5 + N S A * F V K K Q G * V S W L K G L P K F4 + + + Y T D * K F L C K H * L K A V G L E C Y F1 + T P T R N S C A S T N * K R L A * S V T F2 + H R L E I L V Q A L I E S G W P R V L P F3 + tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac + 70 80 90 100 110 120 + ----:----|----:----|----:----|----:----|----:----|----:----| + atgtggctgatctttaagaacacgttcgtgattaactttcgccaaccggatctcacaatg + * V S * F N K H L C * N F A T P R S H * F6 + K C R S S I R T C A S I S L P Q G L T N F5 + V G V L F E Q A L V L Q F R N A * L T V F4 + + + R F V * L S A S L A L I K G S F S L L W F1 + G L Y S * A R L L P * S K V H F L Y F G F2 + V C I A E R V S C P D Q R F I F S T L E F3 + cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg + 130 140 150 160 170 180 + ----:----|----:----|----:----|----:----|----:----|----:----| + gccaaacatatcgactcgcgcagagaacgggactagtttccaagtaaaagagatgaaacc + R N T Y S L A D R A R I L P E N E R S Q F6 + G T Q I A S R T E Q G S * L N M K E V K F5 + P K Y L Q A R R K G Q D F T * K R * K P F4 + + + K T L W K N T T S T S L S P L V C * L L F1 + R R C G R I Q Q V R V S P P W F A D Y W F2 + D V V E E Y N K Y E S L P P G L L I T G F3 + aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg + 190 200 210 220 230 240 + ----:----|----:----|----:----|----:----|----:----|----:----| + ttctgcaacaccttcttatgttgttcatgctcagagaggggggaccaaacgactaatgac + F V N H F F V V L V L R E G R T Q Q N S F6 + S S T T S S Y L L Y S D R G G P K S I V F5 + L R Q P L I C C T R T E G G Q N A S * Q F4 + + + D T V V I P F A T P R N Y L Y E L F S L F1 + I Q L * Y P S Q H R V T I Y M N Y F P F F2 + Y S C N T L R N T A * L S I * I I F P L F3 + gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt + 250 260 270 280 290 300 + ----:----|----:----|----:----|----:----|----:----|----:----| + ctatgtcaacattatgggaagcgttgtggcgcattgatagatatacttaataaaagggaa + S V T T I G K A V G R L * R Y S N N E R F6 + P Y L Q L V R R L V A Y S D I H I I K G F5 + I C N Y Y G E C C R T V I * I F * K G K F4 + + + Y Y M * * V R L * S S F S K S F T V F D F1 + I I C S R F V F N L P L A S L L L F S T F2 + L Y V V G S S L I F L * Q V F Y C F R P F3 + tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac + 310 320 330 340 350 360 + ----:----|----:----|----:----|----:----|----:----|----:----| + ataatatacatcatccaagcagaaattagaaggaaatcgttcagaaaatgacaaaagctg + * * I Y Y T R R * D E K L L D K V T K S F6 + K N Y T T P E D K I K R * C T K * Q K R F5 + I I H L L N T K L R G K A L R K S N E V F4 + + + L N V H V L R L F W I I C G Q F N L R C F1 + S M F M F L G C F G * Y A V S L I F V V F2 + Q C S C S * V V L D N M R S V * S S L F F3 + ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt + 370 380 390 400 410 420 + ----:----|----:----|----:----|----:----|----:----|----:----| + gagttacaagtacaagaatccaacaaaacctattatacgccagtcaaattagaagcaaca + R L T * T R L N N Q I I H P * N L R R Q F6 + G * H E H E * T T K S L I R D T * D E N F5 + E I N M N K P Q K P Y Y A T L K I K T T F4 + + + F F L K Y L F M V * F L V C T C S G A S F1 + S S * N I Y S W F N F W F V L V Q G P V F2 + L L K I F I H G L I F G L Y L F R G Q F F3 + ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt + 430 440 450 460 470 480 + ----:----|----:----|----:----|----:----|----:----|----:----| + aagaagaattttataaataagtaccaaattaaaaaccaaacatgaacaagtccccggtca + K K K F Y K N M T * N K T Q V Q E P A L F6 + N R R L I N I * P K I K P K Y K N L P W F5 + E E * F I * E H N L K Q N T S T * P G T F4 + + + S L F T L F V Y S S S F I F S M I L I * F1 + H Y L L C L Y T A V L L F L V * F * F K F2 + I I Y S V C I Q Q F F Y F * Y D F N L K F3 + tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa + 490 500 510 520 530 540 + ----:----|----:----|----:----|----:----|----:----|----:----| + agtaataaatgagacaaacatatgtcgtcaagaaaataaaaatcatactaaaattaaatt + E N N V R N T Y L L E K I K L I I K I * F6 + N M I * E T Q I C C N K * K * Y S K L K F5 + * * K S Q K Y V A T R K N K T H N * N L F4 + + + N N S N G Q K F1 + T I L M V K X F2 + Q F * W S K X F3 + aacaattctaatggtcaaaaa + 550 560 + ----:----|----:----|- + ttgttaagattaccagttttt + F L E L P * F F6 + F C N * H D F F5 + V I R I T L F F4 + +############################## +Minimum size of ORFs : 1 + +Total ORFs in frame 1 : 10 +Total ORFs in frame 2 : 11 +Total ORFs in frame 3 : 8 +Total ORFs in frame 4 : 14 +Total ORFs in frame 5 : 12 +Total ORFs in frame 6 : 14 + +Total ORFs : 69 +############################## + |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_skipseq_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_skipseq_out.fasta Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,11 @@ +>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt +tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac +cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg +aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg +gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt +tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac +ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt +ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt +tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa +aacaattctaatggtcaaaaa |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_splitter_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_splitter_out.fasta Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,11 @@ +>Sequence_1-561 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt +tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac +cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg +aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg +gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt +tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac +ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt +ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt +tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa +aacaattctaatggtcaaaaa |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_supermatcher_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_supermatcher_out.fasta Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,24 @@ +>hg17 +CCCTAGAGCTTCTGAGCCCTCAACAG--------AGATGAACTGGACTCTCTGCAGCCCC +ACTCTAAATTC-----------CTAAGAGAGAAGTTGATTGACCCAATCAG-------GG +TCAGGAGAAGGAAGGGAGGAGGAAAGGGAG---------GAGAGAAGAGCCTCTTCGTCT +CTTGCCTACCAC--TGGCCAGGCAATTGTAG---------CCAAGGGGGCT-GGAGTGTA +AATGCAAACATAGCC----------ATCAAGGGTt---gtgtatgtgtgtgtgt------ +----gtgtctgtgtgtgtgtatgtgtgtCTCTTGGGTAGGTTAGATCTCCC--------- +---AGGAGGTCCCTAC--TAAACAGACTTAAGCCCGCAAAA---TTTTA--GCTCTCCAG +CCTCACACACTCCACCCCTCTAC-----CATA-------TTGAATCTTCCCAAACCAACT +ATG-GCT---TTCCCTAA-CTCCGGAGcttggcctggaa--------tgccctgcttccc +ct--ctttcccctgg---ggaacgcctgtccttcaggcctcagttca-----cacactgc +ctcccttgca-----aagctct +>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +ccctaca----caga-----ccacagttttcctaa-------tgg---ctttaca--ccg +actagaaattcttgtgcaagcactaattga-aag-cggttggccta--gagtgttaccgg +tttgta------------tagctgagcgcgtctcttgccctgatcaaaggttcattttct +ct--------actttgg--aagacgttgtggaagaatacaacaag-----tacgagtctc +tcccc--------cctggtttgctgattactggatacagt-----------tgtaatacc +cttcgcaacaccgcgtaactatctatat-------gaa--tta-ttttccctttattata +tgtagtaggttcgt-ctttaatcttcctttagc------aagtcttttactgttttcga- +cctca------------atgttcatgttcttaggttgttttggat------------aat +atgcggtcagtt---taatcttcgttgtttcttcttaaaatatttatt--catggtt--- +-taatttt----tggtttgta---cttg---ttcaggggccagttcattatttactctg- +----tttgtatacagcagttct |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_syco_out.syco --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_syco_out.syco Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,484 @@ +SYCO of Sequence from 1 to 561 + + +Frame 1 +Mid base Gribskov value +46 1.007 +49 1.014 +52 1.012 +55 1.002 +58 1.003 +61 0.997 +64 0.998 +67 0.996 +70 1.005 +73 1.006 +76 1.007 +79 1.020 +82 1.008 +85 1.000 +88 0.995 +91 1.005 +94 1.023 +97 1.011 +100 1.008 +103 1.003 +106 1.017 +109 1.028 +112 1.029 +115 1.019 +118 1.013 +121 1.014 +124 1.003 +127 1.003 +130 0.990 +133 0.981 +136 0.975 +139 0.981 +142 0.983 +145 0.981 +148 0.987 +151 1.000 +154 0.989 +157 0.997 +160 0.995 +163 0.998 +166 0.988 +169 0.981 +172 0.993 +175 1.007 +178 1.016 +181 1.016 +184 0.994 +187 1.006 +190 1.017 +193 1.008 +196 1.016 +199 0.995 +202 0.987 +205 0.982 +208 0.983 +211 0.978 +214 0.989 +217 1.000 +220 1.006 +223 1.013 +226 1.008 +229 0.992 +232 1.002 +235 1.002 +238 0.996 +241 0.987 +244 0.988 +247 0.972 +250 0.966 +253 0.973 +256 0.972 +259 0.968 +262 0.956 +265 0.951 +268 0.942 +271 0.923 +274 0.923 +277 0.907 +280 0.897 +283 0.908 +286 0.888 +289 0.896 +292 0.891 +295 0.911 +298 0.923 +301 0.924 +304 0.914 +307 0.904 +310 0.896 +313 0.901 +316 0.910 +319 0.928 +322 0.918 +325 0.914 +328 0.915 +331 0.911 +334 0.910 +337 0.927 +340 0.926 +343 0.917 +346 0.922 +349 0.920 +352 0.917 +355 0.923 +358 0.917 +361 0.926 +364 0.931 +367 0.937 +370 0.937 +373 0.929 +376 0.930 +379 0.931 +382 0.940 +385 0.915 +388 0.908 +391 0.908 +394 0.899 +397 0.909 +400 0.918 +403 0.904 +406 0.896 +409 0.885 +412 0.884 +415 0.884 +418 0.885 +421 0.889 +424 0.889 +427 0.884 +430 0.892 +433 0.903 +436 0.902 +439 0.906 +442 0.900 +445 0.890 +448 0.893 +451 0.903 +454 0.903 +457 0.899 +460 0.910 +463 0.932 +466 0.935 +469 0.925 +472 0.915 +475 0.926 +478 0.925 +481 0.929 +484 0.943 +487 0.934 +490 0.920 +493 0.925 +496 0.925 +499 0.935 +502 0.936 +505 0.939 +508 0.940 +511 0.936 +514 0.932 + + +Frame 2 +Mid base Gribskov value +47 1.003 +50 0.992 +53 1.002 +56 0.997 +59 1.006 +62 1.005 +65 1.007 +68 0.997 +71 1.001 +74 0.996 +77 0.997 +80 0.982 +83 0.975 +86 0.965 +89 0.971 +92 0.977 +95 0.975 +98 0.968 +101 0.979 +104 0.968 +107 0.978 +110 0.982 +113 0.984 +116 0.994 +119 0.984 +122 0.983 +125 0.984 +128 0.996 +131 1.004 +134 0.986 +137 0.992 +140 0.997 +143 0.980 +146 0.972 +149 0.966 +152 0.971 +155 0.956 +158 0.950 +161 0.943 +164 0.944 +167 0.933 +170 0.944 +173 0.944 +176 0.955 +179 0.949 +182 0.944 +185 0.945 +188 0.952 +191 0.941 +194 0.952 +197 0.946 +200 0.934 +203 0.943 +206 0.935 +209 0.940 +212 0.952 +215 0.953 +218 0.937 +221 0.923 +224 0.934 +227 0.938 +230 0.930 +233 0.936 +236 0.949 +239 0.943 +242 0.944 +245 0.946 +248 0.950 +251 0.954 +254 0.968 +257 0.968 +260 0.962 +263 0.960 +266 0.949 +269 0.943 +272 0.946 +275 0.956 +278 0.963 +281 0.963 +284 0.952 +287 0.947 +290 0.950 +293 0.930 +296 0.934 +299 0.936 +302 0.925 +305 0.915 +308 0.939 +311 0.943 +314 0.928 +317 0.930 +320 0.936 +323 0.941 +326 0.938 +329 0.943 +332 0.949 +335 0.939 +338 0.935 +341 0.934 +344 0.924 +347 0.929 +350 0.929 +353 0.932 +356 0.930 +359 0.934 +362 0.930 +365 0.911 +368 0.916 +371 0.925 +374 0.921 +377 0.917 +380 0.916 +383 0.924 +386 0.922 +389 0.919 +392 0.921 +395 0.930 +398 0.912 +401 0.916 +404 0.920 +407 0.909 +410 0.908 +413 0.908 +416 0.898 +419 0.890 +422 0.880 +425 0.885 +428 0.899 +431 0.907 +434 0.912 +437 0.904 +440 0.901 +443 0.901 +446 0.893 +449 0.897 +452 0.894 +455 0.903 +458 0.890 +461 0.886 +464 0.894 +467 0.894 +470 0.894 +473 0.885 +476 0.884 +479 0.875 +482 0.870 +485 0.879 +488 0.878 +491 0.875 +494 0.875 +497 0.876 +500 0.881 +503 0.878 +506 0.876 +509 0.883 +512 0.891 +515 0.896 + + +Frame 3 +Mid base Gribskov value +48 0.929 +51 0.933 +54 0.930 +57 0.946 +60 0.940 +63 0.947 +66 0.947 +69 0.953 +72 0.968 +75 0.950 +78 0.949 +81 0.939 +84 0.929 +87 0.915 +90 0.910 +93 0.922 +96 0.921 +99 0.931 +102 0.925 +105 0.935 +108 0.945 +111 0.935 +114 0.930 +117 0.940 +120 0.949 +123 0.949 +126 0.960 +129 0.944 +132 0.947 +135 0.943 +138 0.946 +141 0.955 +144 0.949 +147 0.948 +150 0.953 +153 0.950 +156 0.960 +159 0.965 +162 0.958 +165 0.979 +168 0.987 +171 0.991 +174 1.003 +177 1.017 +180 1.018 +183 1.004 +186 0.994 +189 1.008 +192 1.010 +195 0.998 +198 1.002 +201 1.013 +204 1.021 +207 1.012 +210 1.002 +213 1.013 +216 1.001 +219 1.012 +222 1.024 +225 1.037 +228 1.035 +231 1.025 +234 1.028 +237 1.011 +240 1.007 +243 1.016 +246 1.006 +249 0.997 +252 0.999 +255 0.989 +258 0.971 +261 0.962 +264 0.950 +267 0.936 +270 0.931 +273 0.931 +276 0.928 +279 0.907 +282 0.897 +285 0.910 +288 0.915 +291 0.904 +294 0.902 +297 0.899 +300 0.905 +303 0.895 +306 0.905 +309 0.896 +312 0.887 +315 0.877 +318 0.879 +321 0.874 +324 0.875 +327 0.878 +330 0.880 +333 0.871 +336 0.871 +339 0.866 +342 0.853 +345 0.851 +348 0.861 +351 0.870 +354 0.874 +357 0.887 +360 0.892 +363 0.892 +366 0.897 +369 0.897 +372 0.903 +375 0.891 +378 0.881 +381 0.881 +384 0.879 +387 0.884 +390 0.875 +393 0.875 +396 0.866 +399 0.865 +402 0.861 +405 0.852 +408 0.852 +411 0.856 +414 0.852 +417 0.850 +420 0.859 +423 0.859 +426 0.867 +429 0.879 +432 0.893 +435 0.903 +438 0.912 +441 0.913 +444 0.910 +447 0.910 +450 0.908 +453 0.908 +456 0.906 +459 0.905 +462 0.918 +465 0.929 +468 0.939 +471 0.940 +474 0.940 +477 0.939 +480 0.943 +483 0.943 +486 0.942 +489 0.943 +492 0.948 +495 0.948 +498 0.948 +501 0.943 +504 0.958 +507 0.960 +510 0.954 +513 0.956 +516 0.947 |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_tranalign_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_tranalign_out.fasta Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,45 @@ +>HSFAU1 +cctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcag +ctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcc +cagatcaaggctcatgtagcctca---ctggagggcattgccccggaagatcaagtcgtg +ctcctggcaggc---cccctggaggatgaggccactctgggccagtgcggggtggaggcc +ctgactaccctggaagtagcaggccgcatgcttgga---ggtaaagttcatggttccctg +gcccgtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaag +aagaagacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtg +cccacctttggcaagaagaagggccccaatgccaactct +>HSFAU2 +cctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcag +ctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcc +cagatcaaggctcatgtagcctca---ctggagggcattgccccggaagatcaagtcgtg +ctcctggcaggcgcgcccctggaggatgcactctgggccagtgcggggtggaggccc--- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------------- +>HSFAU3 +cctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcag +ctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcc +cagatcaaggctcatgtagcctca---ctggagggcattgccccggaagatcaagtcgtg +ctcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggcc +ctgactaccctggaagtagcaggccgcatgcttgga---ggtaaagttcatggttccctg +gcccgtgctggaaaagtgagaggtcagactcctaagggggccaaacaggagaagaagaag +aagaagacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtg +cccacctttggcaagaagaagggccccaatgccaactct +>HSFAU4 +cctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcag +ctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcc +cagatcaaggctcatgaaatagcctcactggagggcattgccccggaagatcaagtcgtg +ctcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggcc +ctgactaccctggaagtagcaggccgcatgcttgcccgaggtaaagttcatggttccctg +gcccgtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaag +aagaagacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtg +cccacctttggcaagaagaagggccccaatgccaactct +>HSFAU5 +cctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcag +ctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcc +cagatcaaggctcatgtagcctca---ctggagggcattgccccggaagatcaagtcgtg +ctcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggcc +ctgactaccctggaagtaggccgcatgctttttgga---ggtaaagttcatggttccctg +gcccgtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaag +aagaagacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtg +cccacctttggcaagaagaagggccccaatgccaactct \ No newline at end of file |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_transeq_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_transeq_out.fasta Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,5 @@ +>Sequence_1 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +VRCLKYLLLSLHRPQFS*WLYTD*KFLCKH*LKAVGLECYRFV*LSASLALIKGSFSLLW +KTLWKNTTSTSLSPLVC*LLDTVVIPFATPRNYLYELFSLYYM**VRL*SSFSKSFTVFD +LNVHVLRLFWIICGQFNLRCFFLKYLFMV*FLVCTCSGASSLFTLFVYSSSFIFSMILI* +NNSNGQK |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_trimest_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_trimest_out.fasta Wed Mar 21 16:30:01 2012 -0400 |
| [ |
| @@ -0,0 +1,11 @@ +>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; [poly-A tail removed] +gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt +tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac +cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg +aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg +gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt +tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac +ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt +ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt +tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa +aacaattctaatggtc |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_trimseq_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_trimseq_out.fasta Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,11 @@ +>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt +tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac +cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg +aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg +gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt +tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac +ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt +ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt +tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa +aacaattctaatggtcaaaaa |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_union_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_union_out.fasta Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,11 @@ +>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt +tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac +cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg +aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg +gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt +tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac +ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt +ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt +tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa +aacaattctaatggtcaaaaa |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_water_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_water_out.fasta Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,32 @@ +>hg17 +GTTTGAAGTTGAGATGTGGGTACAATACCATAGCTTTATTC------CAGAGCAGGGTAT +TTGTTTCCAAATGCCATGTTCCCAGCAGCTGCCCTTGACTGGGAATTGGGGTGTGATTTG +GGCTTTT-----CCTTAAATCCTTGAGGAGCTGGAGGGGTGGGTGGCTCGCACTCCTGCT +TTctggatctgaatcctgactctgtcatggacctgtttgactttgggcaagttgactcct +attcctgagccccatatttttctcttctgtgaaattcagattaaaaAAACATGGCTTTGA +TCAAA----CATTATAAATAATATATAGACAGACTGCTTGTTTTTATTGTATTGCCAGAA +ATGAATCCTACTAATA-------------------TTGC-CATCTA-TGG--ACAGAAAA +TGTATTACCTGTCTTCATCAAGACCCAGACGAGGAAGAACACGAAAAGCGGA-------- +---GATTAATTTTACTGCC-------ATCTCCAGAA---CCGTCATCCTAATATTTACTT +A-CA----TTTTATTATTATTTCAGGCTC-ATGCACATATACTTAG-----CATGGATCA +T-TGGCCACAGACTCGCATACATTTAA-CTTTATTACCTTTTGCCTCATGTATCTCATTA +AAATTTTGCTGCTTAATCAAGGATCTGCATATTATTTTAATTTTAGAATTCACAGTTCCA +AGACTTTGAAAGTTTCAAGCGTTCTGGGTGaatgtgttatgctctctcccgcca--ccat +gtctttataccccctgatttct---cagccactatggcaaccactttctactcttagta- +gcccat----atttagtccaatccccagctcaggagacacttct +>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +gttcga----------tgcctaaaatacctt--cttttgtccctacacagaccacagt-- +---tttcctaatggc---tttacacc----------gactagaaatt------------- +--cttgtgcaagcactaa----ttga-aagc---------ggttggc------------- +--ctaga--------------gtgt----taccggtttg--------------------t +atagctgagcgc-------gtctctt---------------------------gccctga +tcaaaggttcattttctctact---ttggaagac-----------gttgt-------gga +a-gaatacaacaagtacgagtctctcccccctggtttgctgat-tactggatacag---t +tgtaatacc---cttc-gcaacacc----------------------gcgtaactatcta +tatgaattatttt----ccctttattatatgtagtaggttcgtctt--taatcttccttt +agcaagtcttttactgt--tttcgacctcaatgttcatgttcttaggttgttttggataa +tatgcggtcag-----------tttaatcttcgt--------------tgtttcttctta +aaatat------ttattcatgg-------------tttaatttttggttt----gt---- +--actt--------------gttcaggg----------------------gccagttcat +-tattta----ctctg-tttgtatacagc----------agttcttt-tatttttagtat +g---attttaattta-------------------aaacaattct |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_water_out.score --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_water_out.score Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,4 @@ +Sequence hg17 884 (610.5) + +#--------------------------------------- +#--------------------------------------- |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_wobble_out.png |
| b |
| Binary file test-data/emboss_wobble_out.png has changed |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_wobble_out.wobble --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_wobble_out.wobble Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,1 @@ +Expected GC content in third position = 36.36 |
| b |
| diff -r b94ca591877b -r 7334f6d0ac17 test-data/emboss_wordcount_out.wordcount --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_wordcount_out.wordcount Wed Mar 21 16:30:01 2012 -0400 |
| b |
| @@ -0,0 +1,202 @@ +ttta 13 +tttt 13 +tctt 11 +gttt 10 +ttgt 10 +taat 9 +ttct 8 +attt 8 +tttg 8 +gttc 8 +tgtt 8 +ggtt 8 +cttt 8 +aatt 6 +tatt 6 +ttaa 6 +ttat 6 +ttca 5 +ttcg 5 +tttc 5 +cagt 5 +gttg 5 +taca 5 +aata 5 +ccct 5 +agtt 5 +tgta 5 +tact 5 +cttc 5 +atac 5 +ttac 5 +aaaa 5 +atta 4 +tctc 4 +ctaa 4 +gtct 4 +ccta 4 +tata 4 +ctct 4 +cctt 4 +tatg 4 +ttgg 4 +acag 4 +tgga 4 +atat 4 +tcat 4 +tggt 4 +atct 3 +aaat 3 +ttcc 3 +taaa 3 +tcta 3 +attc 3 +tgat 3 +cggt 3 +agca 3 +aaca 3 +cccc 3 +agta 3 +tacc 3 +aatg 3 +caag 3 +cttg 3 +atgg 3 +atgt 3 +acaa 3 +acac 3 +tcaa 3 +aggt 3 +gcaa 3 +ttag 3 +ctga 3 +accg 3 +gtat 3 +acta 3 +tccc 3 +tgaa 2 +tcct 2 +actt 2 +ggaa 2 +gcct 2 +gtca 2 +ctac 2 +gaaa 2 +ctag 2 +gaag 2 +gctg 2 +ggat 2 +ctat 2 +gaat 2 +agcg 2 +tgcc 2 +agtc 2 +aatc 2 +cgac 2 +ggcc 2 +caaa 2 +caac 2 +gacc 2 +cctg 2 +tgtg 2 +caat 2 +ggtc 2 +ctta 2 +gata 2 +atga 2 +atgc 2 +tcga 2 +gatt 2 +gcgg 2 +tcgt 2 +ttgc 2 +gcgt 2 +cgcg 2 +caca 2 +cacc 2 +cgtc 2 +aaga 2 +catg 2 +aagc 2 +cgtt 2 +tcag 2 +catt 2 +aagt 2 +tggc 2 +taga 2 +tagc 2 +tagg 2 +gtaa 2 +ctgg 2 +gtac 2 +gtag 2 +tagt 2 +ctgt 2 +gagt 2 +agaa 2 +agac 2 +acct 2 +aaag 2 +actg 2 +gccc 1 +ccag 1 +tgag 1 +taac 1 +attg 1 +caga 1 +tctg 1 +cagc 1 +gtcc 1 +cagg 1 +gctt 1 +gtta 1 +agct 1 +tgca 1 +aact 1 +tgcg 1 +agtg 1 +tacg 1 +ctca 1 +cgag 1 +ctcc 1 +cctc 1 +tgct 1 +acga 1 +gacg 1 +tgtc 1 +cgat 1 +ggct 1 +tatc 1 +gact 1 +acgt 1 +gatc 1 +tcgc 1 +gatg 1 +gcgc 1 +ttga 1 +cgca 1 +gtgc 1 +gtgg 1 +cgta 1 +gtgt 1 +cact 1 +aggg 1 +ataa 1 +aagg 1 +atag 1 +ccga 1 +ccgc 1 +ccgg 1 +gcac 1 +gcag 1 +gggc 1 +gggg 1 +gagc 1 +acca 1 +accc 1 +atca 1 +agag 1 +aaac 1 +actc 1 +gcca 1 +ccac 1 |
