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comparison test-data/human_augustus_utr-on.gff @ 0:af307d3285c5 draft

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author bgruening
date Sat, 06 Jul 2013 10:07:41 -0400
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-1:000000000000 0:af307d3285c5
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