Mercurial > repos > bgruening > augustus
diff test-data/human_augustus_utr-on.gff @ 0:af307d3285c5 draft
Uploaded
| author | bgruening |
|---|---|
| date | Sat, 06 Jul 2013 10:07:41 -0400 |
| parents | |
| children | f5075dee9d6b |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/human_augustus_utr-on.gff Sat Jul 06 10:07:41 2013 -0400 @@ -0,0 +1,77 @@ +##gff-version 3 +# This output was generated with AUGUSTUS (version 2.7). +# AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke (mario.stanke@uni-greifswald.de) +# and Oliver Keller (keller@cs.uni-goettingen.de). +# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), +# Using native and syntenically mapped cDNA alignments to improve de novo gene finding +# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 +# No extrinsic information on sequences given. +# Initialising the parameters ... +# human version. Using species specific transition matrix: /home/bag/Downloads/augustus.2.7/config/species/human/human_trans_shadow_partial_utr.pbl +# Looks like ./examples/example.fa is in fasta format. +# We have hints for 0 sequences and for 0 of the sequences in the input set. +# +# ----- prediction on sequence number 1 (length = 9453, name = HS04636) ----- +# +# Predicted genes for sequence number 1 on both strands +# start gene g1 +HS04636 AUGUSTUS gene 836 8857 1 + . ID=g1 +HS04636 AUGUSTUS transcript 836 8857 . + . ID=g1.t1;Parent=g1 +HS04636 AUGUSTUS transcription_start_site 836 836 . + . Parent=g1.t1 +HS04636 AUGUSTUS exon 836 1017 . + . Parent=g1.t1 +HS04636 AUGUSTUS start_codon 966 968 . + 0 Parent=g1.t1 +HS04636 AUGUSTUS CDS 966 1017 . + 0 ID=g1.t1.cds;Parent=g1.t1 +HS04636 AUGUSTUS CDS 1818 1934 . + 2 ID=g1.t1.cds;Parent=g1.t1 +HS04636 AUGUSTUS exon 1818 1934 . + . Parent=g1.t1 +HS04636 AUGUSTUS CDS 2055 2198 . + 2 ID=g1.t1.cds;Parent=g1.t1 +HS04636 AUGUSTUS exon 2055 2198 . + . Parent=g1.t1 +HS04636 AUGUSTUS CDS 2852 2995 . + 2 ID=g1.t1.cds;Parent=g1.t1 +HS04636 AUGUSTUS exon 2852 2995 . + . Parent=g1.t1 +HS04636 AUGUSTUS CDS 3426 3607 . + 2 ID=g1.t1.cds;Parent=g1.t1 +HS04636 AUGUSTUS exon 3426 3607 . + . Parent=g1.t1 +HS04636 AUGUSTUS CDS 4340 4423 . + 0 ID=g1.t1.cds;Parent=g1.t1 +HS04636 AUGUSTUS exon 4340 4423 . + . Parent=g1.t1 +HS04636 AUGUSTUS CDS 4543 4789 . + 0 ID=g1.t1.cds;Parent=g1.t1 +HS04636 AUGUSTUS exon 4543 4789 . + . Parent=g1.t1 +HS04636 AUGUSTUS CDS 5072 5358 . + 2 ID=g1.t1.cds;Parent=g1.t1 +HS04636 AUGUSTUS exon 5072 5358 . + . Parent=g1.t1 +HS04636 AUGUSTUS CDS 5860 6007 . + 0 ID=g1.t1.cds;Parent=g1.t1 +HS04636 AUGUSTUS exon 5860 6007 . + . Parent=g1.t1 +HS04636 AUGUSTUS CDS 6494 6903 . + 2 ID=g1.t1.cds;Parent=g1.t1 +HS04636 AUGUSTUS exon 6494 8857 . + . Parent=g1.t1 +HS04636 AUGUSTUS stop_codon 6901 6903 . + 0 Parent=g1.t1 +HS04636 AUGUSTUS transcription_end_site 8857 8857 . + . Parent=g1.t1 +# protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL +# THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD +# PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG +# QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH +# WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE +# KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV +# PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL] +# end gene g1 +### +# +# ----- prediction on sequence number 2 (length = 2344, name = HS08198) ----- +# +# Predicted genes for sequence number 2 on both strands +# start gene g2 +HS08198 AUGUSTUS gene 86 2344 1 + . ID=g2 +HS08198 AUGUSTUS transcript 86 2344 . + . ID=g2.t1;Parent=g2 +HS08198 AUGUSTUS transcription_start_site 86 86 . + . Parent=g2.t1 +HS08198 AUGUSTUS exon 86 582 . + . Parent=g2.t1 +HS08198 AUGUSTUS start_codon 445 447 . + 0 Parent=g2.t1 +HS08198 AUGUSTUS CDS 445 582 . + 0 ID=g2.t1.cds;Parent=g2.t1 +HS08198 AUGUSTUS CDS 812 894 . + 0 ID=g2.t1.cds;Parent=g2.t1 +HS08198 AUGUSTUS exon 812 894 . + . Parent=g2.t1 +HS08198 AUGUSTUS CDS 1053 1123 . + 1 ID=g2.t1.cds;Parent=g2.t1 +HS08198 AUGUSTUS exon 1053 1123 . + . Parent=g2.t1 +HS08198 AUGUSTUS CDS 1208 1315 . + 2 ID=g2.t1.cds;Parent=g2.t1 +HS08198 AUGUSTUS exon 1208 1315 . + . Parent=g2.t1 +HS08198 AUGUSTUS CDS 1587 1688 . + 2 ID=g2.t1.cds;Parent=g2.t1 +HS08198 AUGUSTUS exon 1587 1688 . + . Parent=g2.t1 +# protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC +# WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKY] +# end gene g2 +### +# command line: +# ./bin/augustus --species=human --UTR=on --gff3=on ./examples/example.fa