Mercurial > repos > bgruening > augustus
comparison test-data/human_augustus_utr-on.gff @ 0:af307d3285c5 draft
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author | bgruening |
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date | Sat, 06 Jul 2013 10:07:41 -0400 |
parents | |
children | f5075dee9d6b |
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-1:000000000000 | 0:af307d3285c5 |
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1 ##gff-version 3 | |
2 # This output was generated with AUGUSTUS (version 2.7). | |
3 # AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke (mario.stanke@uni-greifswald.de) | |
4 # and Oliver Keller (keller@cs.uni-goettingen.de). | |
5 # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), | |
6 # Using native and syntenically mapped cDNA alignments to improve de novo gene finding | |
7 # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 | |
8 # No extrinsic information on sequences given. | |
9 # Initialising the parameters ... | |
10 # human version. Using species specific transition matrix: /home/bag/Downloads/augustus.2.7/config/species/human/human_trans_shadow_partial_utr.pbl | |
11 # Looks like ./examples/example.fa is in fasta format. | |
12 # We have hints for 0 sequences and for 0 of the sequences in the input set. | |
13 # | |
14 # ----- prediction on sequence number 1 (length = 9453, name = HS04636) ----- | |
15 # | |
16 # Predicted genes for sequence number 1 on both strands | |
17 # start gene g1 | |
18 HS04636 AUGUSTUS gene 836 8857 1 + . ID=g1 | |
19 HS04636 AUGUSTUS transcript 836 8857 . + . ID=g1.t1;Parent=g1 | |
20 HS04636 AUGUSTUS transcription_start_site 836 836 . + . Parent=g1.t1 | |
21 HS04636 AUGUSTUS exon 836 1017 . + . Parent=g1.t1 | |
22 HS04636 AUGUSTUS start_codon 966 968 . + 0 Parent=g1.t1 | |
23 HS04636 AUGUSTUS CDS 966 1017 . + 0 ID=g1.t1.cds;Parent=g1.t1 | |
24 HS04636 AUGUSTUS CDS 1818 1934 . + 2 ID=g1.t1.cds;Parent=g1.t1 | |
25 HS04636 AUGUSTUS exon 1818 1934 . + . Parent=g1.t1 | |
26 HS04636 AUGUSTUS CDS 2055 2198 . + 2 ID=g1.t1.cds;Parent=g1.t1 | |
27 HS04636 AUGUSTUS exon 2055 2198 . + . Parent=g1.t1 | |
28 HS04636 AUGUSTUS CDS 2852 2995 . + 2 ID=g1.t1.cds;Parent=g1.t1 | |
29 HS04636 AUGUSTUS exon 2852 2995 . + . Parent=g1.t1 | |
30 HS04636 AUGUSTUS CDS 3426 3607 . + 2 ID=g1.t1.cds;Parent=g1.t1 | |
31 HS04636 AUGUSTUS exon 3426 3607 . + . Parent=g1.t1 | |
32 HS04636 AUGUSTUS CDS 4340 4423 . + 0 ID=g1.t1.cds;Parent=g1.t1 | |
33 HS04636 AUGUSTUS exon 4340 4423 . + . Parent=g1.t1 | |
34 HS04636 AUGUSTUS CDS 4543 4789 . + 0 ID=g1.t1.cds;Parent=g1.t1 | |
35 HS04636 AUGUSTUS exon 4543 4789 . + . Parent=g1.t1 | |
36 HS04636 AUGUSTUS CDS 5072 5358 . + 2 ID=g1.t1.cds;Parent=g1.t1 | |
37 HS04636 AUGUSTUS exon 5072 5358 . + . Parent=g1.t1 | |
38 HS04636 AUGUSTUS CDS 5860 6007 . + 0 ID=g1.t1.cds;Parent=g1.t1 | |
39 HS04636 AUGUSTUS exon 5860 6007 . + . Parent=g1.t1 | |
40 HS04636 AUGUSTUS CDS 6494 6903 . + 2 ID=g1.t1.cds;Parent=g1.t1 | |
41 HS04636 AUGUSTUS exon 6494 8857 . + . Parent=g1.t1 | |
42 HS04636 AUGUSTUS stop_codon 6901 6903 . + 0 Parent=g1.t1 | |
43 HS04636 AUGUSTUS transcription_end_site 8857 8857 . + . Parent=g1.t1 | |
44 # protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL | |
45 # THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD | |
46 # PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG | |
47 # QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH | |
48 # WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE | |
49 # KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV | |
50 # PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL] | |
51 # end gene g1 | |
52 ### | |
53 # | |
54 # ----- prediction on sequence number 2 (length = 2344, name = HS08198) ----- | |
55 # | |
56 # Predicted genes for sequence number 2 on both strands | |
57 # start gene g2 | |
58 HS08198 AUGUSTUS gene 86 2344 1 + . ID=g2 | |
59 HS08198 AUGUSTUS transcript 86 2344 . + . ID=g2.t1;Parent=g2 | |
60 HS08198 AUGUSTUS transcription_start_site 86 86 . + . Parent=g2.t1 | |
61 HS08198 AUGUSTUS exon 86 582 . + . Parent=g2.t1 | |
62 HS08198 AUGUSTUS start_codon 445 447 . + 0 Parent=g2.t1 | |
63 HS08198 AUGUSTUS CDS 445 582 . + 0 ID=g2.t1.cds;Parent=g2.t1 | |
64 HS08198 AUGUSTUS CDS 812 894 . + 0 ID=g2.t1.cds;Parent=g2.t1 | |
65 HS08198 AUGUSTUS exon 812 894 . + . Parent=g2.t1 | |
66 HS08198 AUGUSTUS CDS 1053 1123 . + 1 ID=g2.t1.cds;Parent=g2.t1 | |
67 HS08198 AUGUSTUS exon 1053 1123 . + . Parent=g2.t1 | |
68 HS08198 AUGUSTUS CDS 1208 1315 . + 2 ID=g2.t1.cds;Parent=g2.t1 | |
69 HS08198 AUGUSTUS exon 1208 1315 . + . Parent=g2.t1 | |
70 HS08198 AUGUSTUS CDS 1587 1688 . + 2 ID=g2.t1.cds;Parent=g2.t1 | |
71 HS08198 AUGUSTUS exon 1587 1688 . + . Parent=g2.t1 | |
72 # protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC | |
73 # WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKY] | |
74 # end gene g2 | |
75 ### | |
76 # command line: | |
77 # ./bin/augustus --species=human --UTR=on --gff3=on ./examples/example.fa |