|
5
|
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 # Initialising the parameters ...
|
|
|
9 # human version. Using species specific transition matrix: /home/bag/Downloads/augustus.2.7/config/species/human/human_trans_shadow_partial_utr.pbl
|
|
|
10 # Looks like ./examples/example.fa is in fasta format.
|
|
|
11 # We have hints for 0 sequences and for 0 of the sequences in the input set.
|
|
|
12 #
|
|
|
13 # ----- prediction on sequence number 1 (length = 9453, name = HS04636) -----
|
|
|
14 #
|
|
|
15 # Constraints/Hints:
|
|
|
16 # (none)
|
|
|
17 # Predicted genes for sequence number 1 on both strands
|
|
|
18 # start gene g1
|
|
|
19 HS04636 AUGUSTUS gene 836 8857 1 + . g1
|
|
|
20 HS04636 AUGUSTUS transcript 836 8857 . + . g1.t1
|
|
|
21 HS04636 AUGUSTUS tss 836 836 . + . transcript_id "g1.t1"; gene_id "g1";
|
|
|
22 HS04636 AUGUSTUS exon 836 1017 . + . transcript_id "g1.t1"; gene_id "g1";
|
|
|
23 HS04636 AUGUSTUS start_codon 966 968 . + 0 transcript_id "g1.t1"; gene_id "g1";
|
|
|
24 HS04636 AUGUSTUS CDS 966 1017 . + 0 transcript_id "g1.t1"; gene_id "g1";
|
|
|
25 HS04636 AUGUSTUS CDS 1818 1934 . + 2 transcript_id "g1.t1"; gene_id "g1";
|
|
|
26 HS04636 AUGUSTUS exon 1818 1934 . + . transcript_id "g1.t1"; gene_id "g1";
|
|
|
27 HS04636 AUGUSTUS CDS 2055 2198 . + 2 transcript_id "g1.t1"; gene_id "g1";
|
|
|
28 HS04636 AUGUSTUS exon 2055 2198 . + . transcript_id "g1.t1"; gene_id "g1";
|
|
|
29 HS04636 AUGUSTUS CDS 2852 2995 . + 2 transcript_id "g1.t1"; gene_id "g1";
|
|
|
30 HS04636 AUGUSTUS exon 2852 2995 . + . transcript_id "g1.t1"; gene_id "g1";
|
|
|
31 HS04636 AUGUSTUS CDS 3426 3607 . + 2 transcript_id "g1.t1"; gene_id "g1";
|
|
|
32 HS04636 AUGUSTUS exon 3426 3607 . + . transcript_id "g1.t1"; gene_id "g1";
|
|
|
33 HS04636 AUGUSTUS CDS 4340 4423 . + 0 transcript_id "g1.t1"; gene_id "g1";
|
|
|
34 HS04636 AUGUSTUS exon 4340 4423 . + . transcript_id "g1.t1"; gene_id "g1";
|
|
|
35 HS04636 AUGUSTUS CDS 4543 4789 . + 0 transcript_id "g1.t1"; gene_id "g1";
|
|
|
36 HS04636 AUGUSTUS exon 4543 4789 . + . transcript_id "g1.t1"; gene_id "g1";
|
|
|
37 HS04636 AUGUSTUS CDS 5072 5358 . + 2 transcript_id "g1.t1"; gene_id "g1";
|
|
|
38 HS04636 AUGUSTUS exon 5072 5358 . + . transcript_id "g1.t1"; gene_id "g1";
|
|
|
39 HS04636 AUGUSTUS CDS 5860 6007 . + 0 transcript_id "g1.t1"; gene_id "g1";
|
|
|
40 HS04636 AUGUSTUS exon 5860 6007 . + . transcript_id "g1.t1"; gene_id "g1";
|
|
|
41 HS04636 AUGUSTUS CDS 6494 6903 . + 2 transcript_id "g1.t1"; gene_id "g1";
|
|
|
42 HS04636 AUGUSTUS exon 6494 8857 . + . transcript_id "g1.t1"; gene_id "g1";
|
|
|
43 HS04636 AUGUSTUS stop_codon 6901 6903 . + 0 transcript_id "g1.t1"; gene_id "g1";
|
|
|
44 HS04636 AUGUSTUS tts 8857 8857 . + . transcript_id "g1.t1"; gene_id "g1";
|
|
|
45 # protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL
|
|
|
46 # THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD
|
|
|
47 # PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG
|
|
|
48 # QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH
|
|
|
49 # WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE
|
|
|
50 # KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV
|
|
|
51 # PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]
|
|
|
52 # end gene g1
|
|
|
53 ###
|
|
|
54 #
|
|
|
55 # ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
|
|
|
56 #
|
|
|
57 # Constraints/Hints:
|
|
|
58 # (none)
|
|
|
59 # Predicted genes for sequence number 2 on both strands
|
|
|
60 # start gene g2
|
|
|
61 HS08198 AUGUSTUS gene 86 2344 1 + . g2
|
|
|
62 HS08198 AUGUSTUS transcript 86 2344 . + . g2.t1
|
|
|
63 HS08198 AUGUSTUS tss 86 86 . + . transcript_id "g2.t1"; gene_id "g2";
|
|
|
64 HS08198 AUGUSTUS exon 86 582 . + . transcript_id "g2.t1"; gene_id "g2";
|
|
|
65 HS08198 AUGUSTUS start_codon 445 447 . + 0 transcript_id "g2.t1"; gene_id "g2";
|
|
|
66 HS08198 AUGUSTUS CDS 445 582 . + 0 transcript_id "g2.t1"; gene_id "g2";
|
|
|
67 HS08198 AUGUSTUS CDS 812 894 . + 0 transcript_id "g2.t1"; gene_id "g2";
|
|
|
68 HS08198 AUGUSTUS exon 812 894 . + . transcript_id "g2.t1"; gene_id "g2";
|
|
|
69 HS08198 AUGUSTUS CDS 1053 1123 . + 1 transcript_id "g2.t1"; gene_id "g2";
|
|
|
70 HS08198 AUGUSTUS exon 1053 1123 . + . transcript_id "g2.t1"; gene_id "g2";
|
|
|
71 HS08198 AUGUSTUS CDS 1208 1315 . + 2 transcript_id "g2.t1"; gene_id "g2";
|
|
|
72 HS08198 AUGUSTUS exon 1208 1315 . + . transcript_id "g2.t1"; gene_id "g2";
|
|
|
73 HS08198 AUGUSTUS CDS 1587 1688 . + 2 transcript_id "g2.t1"; gene_id "g2";
|
|
|
74 HS08198 AUGUSTUS exon 1587 1688 . + . transcript_id "g2.t1"; gene_id "g2";
|
|
|
75 # protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC
|
|
|
76 # WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKY]
|
|
|
77 # end gene g2
|
|
|
78 ###
|
|
|
79 # command line:
|
|
|
80 # ./bin/augustus --species=human --UTR=on ./examples/example.fa
|
