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comparison test-data/human_augustus_protein_codingseq_introns_cds_main.gtf @ 5:a4fab0c1ae1a

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author bjoern-gruening
date Sun, 09 Jun 2013 07:54:25 -0400
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1 # This output was generated with AUGUSTUS (version 2.7).
2 # AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke (mario.stanke@uni-greifswald.de)
3 # and Oliver Keller (keller@cs.uni-goettingen.de).
4 # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
5 # Using native and syntenically mapped cDNA alignments to improve de novo gene finding
6 # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
7 # No extrinsic information on sequences given.
8 # Initialising the parameters ...
9 # human version. Using default transition matrix.
10 # Looks like /home/bag/projects/galaxy/galaxy-central/database/files/001/dataset_1149.dat is in fasta format.
11 # We have hints for 0 sequences and for 0 of the sequences in the input set.
12 #
13 # ----- prediction on sequence number 1 (length = 9453, name = HS04636) -----
14 #
15 # Constraints/Hints:
16 # (none)
17 # Predicted genes for sequence number 1 on both strands
18 # start gene g1
19 HS04636 AUGUSTUS gene 966 6903 1 + . g1
20 HS04636 AUGUSTUS transcript 966 6903 . + . g1.t1
21 HS04636 AUGUSTUS intron 1018 1817 . + . transcript_id "g1.t1"; gene_id "g1";
22 HS04636 AUGUSTUS intron 1935 2054 . + . transcript_id "g1.t1"; gene_id "g1";
23 HS04636 AUGUSTUS intron 2199 2851 . + . transcript_id "g1.t1"; gene_id "g1";
24 HS04636 AUGUSTUS intron 2996 3425 . + . transcript_id "g1.t1"; gene_id "g1";
25 HS04636 AUGUSTUS intron 3608 4339 . + . transcript_id "g1.t1"; gene_id "g1";
26 HS04636 AUGUSTUS intron 4424 4542 . + . transcript_id "g1.t1"; gene_id "g1";
27 HS04636 AUGUSTUS intron 4790 5071 . + . transcript_id "g1.t1"; gene_id "g1";
28 HS04636 AUGUSTUS intron 5359 5859 . + . transcript_id "g1.t1"; gene_id "g1";
29 HS04636 AUGUSTUS intron 6008 6493 . + . transcript_id "g1.t1"; gene_id "g1";
30 HS04636 AUGUSTUS CDS 966 1017 . + 0 transcript_id "g1.t1"; gene_id "g1";
31 HS04636 AUGUSTUS CDS 1818 1934 . + 2 transcript_id "g1.t1"; gene_id "g1";
32 HS04636 AUGUSTUS CDS 2055 2198 . + 2 transcript_id "g1.t1"; gene_id "g1";
33 HS04636 AUGUSTUS CDS 2852 2995 . + 2 transcript_id "g1.t1"; gene_id "g1";
34 HS04636 AUGUSTUS CDS 3426 3607 . + 2 transcript_id "g1.t1"; gene_id "g1";
35 HS04636 AUGUSTUS CDS 4340 4423 . + 0 transcript_id "g1.t1"; gene_id "g1";
36 HS04636 AUGUSTUS CDS 4543 4789 . + 0 transcript_id "g1.t1"; gene_id "g1";
37 HS04636 AUGUSTUS CDS 5072 5358 . + 2 transcript_id "g1.t1"; gene_id "g1";
38 HS04636 AUGUSTUS CDS 5860 6007 . + 0 transcript_id "g1.t1"; gene_id "g1";
39 HS04636 AUGUSTUS CDS 6494 6903 . + 2 transcript_id "g1.t1"; gene_id "g1";
40 # coding sequence = [atgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacagcaaatccttgctgttcccacccatgtc
41 # aaaaccgaggtgtatgtatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggagaaaactgctcaacaccggaattt
42 # ttgacaagaataaaattatttctgaaacccactccaaacacagtgcactacatacttacccacttcaagggattttggaacgttgtgaataacattcc
43 # cttccttcgaaatgcaattatgagttatgtcttgacatccagatcacatttgattgacagtccaccaacttacaatgctgactatggctacaaaagct
44 # gggaagccttctctaacctctcctattatactagagcccttcctcctgtgcctgatgattgcccgactcccttgggtgtcaaaggtaaaaagcagctt
45 # cctgattcaaatgagattgtggaaaaattgcttctaagaagaaagttcatccctgatccccagggctcaaacatgatgtttgcattctttgcccagca
46 # cttcacgcatcagtttttcaagacagatcataagcgagggccagctttcaccaacgggctgggccatggggtggacttaaatcatatttacggtgaaa
47 # ctctggctagacagcgtaaactgcgccttttcaaggatggaaaaatgaaatatcagataattgatggagagatgtatcctcccacagtcaaagatact
48 # caggcagagatgatctaccctcctcaagtccctgagcatctacggtttgctgtggggcaggaggtctttggtctggtgcctggtctgatgatgtatgc
49 # cacaatctggctgcgggaacacaacagagtatgcgatgtgcttaaacaggagcatcctgaatggggtgatgagcagttgttccagacaagcaggctaa
50 # tactgataggagagactattaagattgtgattgaagattatgtgcaacacttgagtggctatcacttcaaactgaaatttgacccagaactacttttc
51 # aacaaacaattccagtaccaaaatcgtattgctgctgaatttaacaccctctatcactggcatccccttctgcctgacacctttcaaattcatgacca
52 # gaaatacaactatcaacagtttatctacaacaactctatattgctggaacatggaattacccagtttgttgaatcattcaccaggcaaattgctggca
53 # gggttgctggtggtaggaatgttccacccgcagtacagaaagtatcacaggcttccattgaccagagcaggcagatgaaataccagtcttttaatgag
54 # taccgcaaacgctttatgctgaagccctatgaatcatttgaagaacttacaggagaaaaggaaatgtctgcagagttggaagcactctatggtgacat
55 # cgatgctgtggagctgtatcctgcccttctggtagaaaagcctcggccagatgccatctttggtgaaaccatggtagaagttggagcaccattctcct
56 # tgaaaggacttatgggtaatgttatatgttctcctgcctactggaagccaagcacttttggtggagaagtgggttttcaaatcatcaacactgcctca
57 # attcagtctctcatctgcaataacgtgaagggctgtccctttacttcattcagtgttccagatccagagctcattaaaacagtcaccatcaatgcaag
58 # ttcttcccgctccggactagatgatatcaatcccacagtactactaaaagaacgttcgactgaactgtag]
59 # protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL
60 # THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD
61 # PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG
62 # QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH
63 # WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE
64 # KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV
65 # PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]
66 # end gene g1
67 ###
68 #
69 # ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
70 #
71 # Constraints/Hints:
72 # (none)
73 # Predicted genes for sequence number 2 on both strands
74 # start gene g2
75 HS08198 AUGUSTUS gene 445 1848 1 + . g2
76 HS08198 AUGUSTUS transcript 445 1848 . + . g2.t1
77 HS08198 AUGUSTUS intron 583 811 . + . transcript_id "g2.t1"; gene_id "g2";
78 HS08198 AUGUSTUS intron 895 1052 . + . transcript_id "g2.t1"; gene_id "g2";
79 HS08198 AUGUSTUS intron 1124 1207 . + . transcript_id "g2.t1"; gene_id "g2";
80 HS08198 AUGUSTUS intron 1316 1586 . + . transcript_id "g2.t1"; gene_id "g2";
81 HS08198 AUGUSTUS intron 1689 1771 . + . transcript_id "g2.t1"; gene_id "g2";
82 HS08198 AUGUSTUS CDS 445 582 . + 0 transcript_id "g2.t1"; gene_id "g2";
83 HS08198 AUGUSTUS CDS 812 894 . + 0 transcript_id "g2.t1"; gene_id "g2";
84 HS08198 AUGUSTUS CDS 1053 1123 . + 1 transcript_id "g2.t1"; gene_id "g2";
85 HS08198 AUGUSTUS CDS 1208 1315 . + 2 transcript_id "g2.t1"; gene_id "g2";
86 HS08198 AUGUSTUS CDS 1587 1688 . + 2 transcript_id "g2.t1"; gene_id "g2";
87 HS08198 AUGUSTUS CDS 1772 1848 . + 2 transcript_id "g2.t1"; gene_id "g2";
88 # coding sequence = [atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccac
89 # gccggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgaggccaccacactgcatgtg
90 # gctccccagggcacagccatggctgtcagtaccttccgaaagctggatgggatctgctggcaggtgcgccagctctatggagacacaggggtcctcgg
91 # ccgcttcctgcttcaagcccgaggcgcccgaggggctgtgcacgtggttgtcgctgagaccgactaccagagtttcgctgtcctgtacctggagcggg
92 # cggggcagctgtcagtgaagctctacgcccgctcgctccctgtgagcgactcggtcctgagtgggtttgagcagcgggtccaggaggcccacctgact
93 # gaggaccagatcttctacttccccaagtacggcttctgcgaggctgcagaccagttccacgtcctggacggtgagtgcacagcgggggcaagcatggc
94 # ggcgtggtga]
95 # protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC
96 # WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF
97 # HVLDGECTAGASMAAW]
98 # end gene g2
99 ###
100 # command line:
101 # augustus --strand=both --noInFrameStop=false --gff3=off --protein=on --introns=on --start=off --stop=off --cds=on --codingseq=on --singlestrand=false /home/bag/projects/galaxy/galaxy-central/database/files/001/dataset_1149.dat --UTR=off --genemodel=complete --species=human