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view 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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##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