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comparison test-data/arabidopsis_augustus_utr-off_singlestrand-on_mea-on.gtf @ 0:af307d3285c5 draft

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author bgruening
date Sat, 06 Jul 2013 10:07:41 -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 # arabidopsis version. Using default transition matrix.
9 # We have hints for 0 sequences and for 0 of the sequences in the input set.
10 #
11 # ----- prediction on sequence number 1 (length = 2066, name = arabidopsis) -----
12 #
13 # Constraints/Hints:
14 # (none)
15 # Predicted genes for sequence number 1 on both strands
16 # start gene g1
17 arabidopsis AUGUSTUS gene 775 1851 0 + . g1
18 arabidopsis AUGUSTUS transcript 775 1851 . + . g1.t1
19 arabidopsis AUGUSTUS start_codon 775 777 . + 0 transcript_id "g1.t1"; gene_id "g1";
20 arabidopsis AUGUSTUS CDS 775 1851 0.99 + 0 transcript_id "g1.t1"; gene_id "g1";
21 arabidopsis AUGUSTUS stop_codon 1849 1851 . + 0 transcript_id "g1.t1"; gene_id "g1";
22 # protein sequence = [MDLSLAPTTTTSSDQEQDRDQELTSNIGASSSSGPSGNNNNLPMMMIPPPEKEHMFDKVVTPSDVGKLNRLVIPKQHA
23 # ERYFPLDSSNNQNGTLLNFQDRNGKMWRFRYSYWNSSQSYVMTKGWSRFVKEKKLDAGDIVSFQRGIGDESERSKLYIDWRHRPDMSLVQAHQFGNFG
24 # FNFNFPTTSQYSNRFHPLPEYNSVPIHRGLNIGNHQRSYYNTQRQEFVGYGYGNLAGRCYYTGSPLDHRNIVGSEPLVIDSVPVVPGRLTPVMLPPLP
25 # PPPSTAGKRLRLFGVNMECGNDYNQQEESWLVPRGEIGASSSSSSALRLNLSTDHDDDNDDGDDGDDDQFAKKGKSSLSLNFNP]
26 # end gene g1
27 ###
28 # start gene g2
29 arabidopsis AUGUSTUS gene 841 1661 . - . g2
30 arabidopsis AUGUSTUS transcript 841 1661 . - . g2.t1
31 arabidopsis AUGUSTUS stop_codon 841 843 . - 0 transcript_id "g2.t1"; gene_id "g2";
32 arabidopsis AUGUSTUS intron 1024 1101 0.75 - . transcript_id "g2.t1"; gene_id "g2";
33 arabidopsis AUGUSTUS intron 1193 1325 0.03 - . transcript_id "g2.t1"; gene_id "g2";
34 arabidopsis AUGUSTUS intron 1416 1512 0.85 - . transcript_id "g2.t1"; gene_id "g2";
35 arabidopsis AUGUSTUS CDS 841 1023 0.87 - 0 transcript_id "g2.t1"; gene_id "g2";
36 arabidopsis AUGUSTUS CDS 1102 1192 0.78 - 1 transcript_id "g2.t1"; gene_id "g2";
37 arabidopsis AUGUSTUS CDS 1326 1415 0.05 - 1 transcript_id "g2.t1"; gene_id "g2";
38 arabidopsis AUGUSTUS CDS 1513 1661 0.35 - 0 transcript_id "g2.t1"; gene_id "g2";
39 # protein sequence = [SLPHSIFTPKSLSLFPAVEGGGGSGGNITGVNLPGTTGTESITNGSDPTMNVGDFRCLSPGESGRSYILAMDEICWNI
40 # EKDNVSCIELFLFDETAPSFGHNVALARVPIRREIPLSVLFRDHESVEFSDVAWCYHFVEHVFFLRRWNHHHRKVVVVSAGTGAAACSDVGG]
41 # end gene g2
42 ###
43 #
44 # ----- prediction on sequence number 2 (length = 1802, name = arabidopsis2) -----
45 #
46 # Constraints/Hints:
47 # (none)
48 # Predicted genes for sequence number 2 on both strands
49 # start gene g3
50 arabidopsis2 AUGUSTUS gene 97 1600 . - . g3
51 arabidopsis2 AUGUSTUS transcript 97 1600 . - . g3.t1
52 arabidopsis2 AUGUSTUS stop_codon 97 99 . - 0 transcript_id "g3.t1"; gene_id "g3";
53 arabidopsis2 AUGUSTUS intron 349 521 0.73 - . transcript_id "g3.t1"; gene_id "g3";
54 arabidopsis2 AUGUSTUS intron 1210 1333 0.36 - . transcript_id "g3.t1"; gene_id "g3";
55 arabidopsis2 AUGUSTUS intron 1452 1560 0.54 - . transcript_id "g3.t1"; gene_id "g3";
56 arabidopsis2 AUGUSTUS CDS 97 348 0.73 - 0 transcript_id "g3.t1"; gene_id "g3";
57 arabidopsis2 AUGUSTUS CDS 522 1209 0.6 - 1 transcript_id "g3.t1"; gene_id "g3";
58 arabidopsis2 AUGUSTUS CDS 1334 1451 0.44 - 2 transcript_id "g3.t1"; gene_id "g3";
59 arabidopsis2 AUGUSTUS CDS 1561 1600 0.42 - 0 transcript_id "g3.t1"; gene_id "g3";
60 arabidopsis2 AUGUSTUS start_codon 1598 1600 . - 0 transcript_id "g3.t1"; gene_id "g3";
61 # protein sequence = [MVKLVFSDLSCAFASANSTASSTNSSIFFSIDFSSASFASLFSIKYFFNAAIGITELIGISQGVSSESISLTFNQGWT
62 # FSSSSSSDSFFSDFPDLQDIHTVNMNTRHPKCRTFLPNLGVRSGSQVRHPNGPQVILDNKDNRQFIESSHVETLEELSVVTSSISEKGDSDIITILFQ
63 # DFPPVLGAKGSTSGDRNAFTNKSKATKHVVFFGEHVHGSTLASAASSNLAEELAHNSTSRDTFAEGMDMVTVGTNDRVRLGKELDKASRNSLLAIVQV
64 # NKTKHLASAGIIGGLLLLDNFLDRDDGRSTGGVGVIESAKGEGTGGSEERRRRSQSDREQETILMGSMQRNRGSELSGSESRRHCYQWKPQ]
65 # end gene g3
66 ###
67 # start gene g4
68 arabidopsis2 AUGUSTUS gene 121 1582 0 + . g4
69 arabidopsis2 AUGUSTUS transcript 121 1582 . + . g4.t1
70 arabidopsis2 AUGUSTUS start_codon 121 123 . + 0 transcript_id "g4.t1"; gene_id "g4";
71 arabidopsis2 AUGUSTUS intron 352 434 0.97 + . transcript_id "g4.t1"; gene_id "g4";
72 arabidopsis2 AUGUSTUS intron 1213 1304 1 + . transcript_id "g4.t1"; gene_id "g4";
73 arabidopsis2 AUGUSTUS CDS 121 351 0.72 + 0 transcript_id "g4.t1"; gene_id "g4";
74 arabidopsis2 AUGUSTUS CDS 435 1212 0.97 + 0 transcript_id "g4.t1"; gene_id "g4";
75 arabidopsis2 AUGUSTUS CDS 1305 1582 1 + 2 transcript_id "g4.t1"; gene_id "g4";
76 arabidopsis2 AUGUSTUS stop_codon 1580 1582 . + 0 transcript_id "g4.t1"; gene_id "g4";
77 # protein sequence = [MATAFAPTKLTATVPLHGSHENRLLLPIRLAPPSSFLGSTRSLSLRRLNHSNATRRSPVVSVQEVVKEKQSTNNTSLL
78 # ITKEEGLELYEDMILGRSFEDMCAQMYYRGKMFGFVHLYNGQEAVSTGFIKLLTKSDSVVSTYRDHVHALSKGVSARAVMSELFGKVTGCCRGQGGSM
79 # HMFSKEHNMLGGFAFIGEGIPVATGAAFSSKYRREVLKQDCDDVTVAFFGDGTCNNGQFFECLNMAALYKLPIIFVVENNLWAIGMSHLRATSDPEIW
80 # KKGPAFGMPGVHVDGMDVLKVREVAKEAVTRARRGEGPTLVECETYRFRGHSLADPDELRDAAEKAKYAARDPIAALKKYLIENKLAKEAELKSIEKK
81 # IDELVEEAVEFADASPQPGRSQLLENVFADPKGFGIGPDGRYRCEDPKFTEGTAQV]
82 # end gene g4
83 ###
84 # command line:
85 # ./bin/augustus --species=arabidopsis --UTR=off --singlestrand=true --mea=1 /home/bag/projects/github/galaxytools/augustus/test-data/arabidopsis_augustus.fa