1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
|
##gff-version 3
# This output was generated with AUGUSTUS (version 2.5).
# 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.
# Initializing the parameters ...
# Using protein profile unknown
# --[8..1336]--> unknown_A (9) <--[16..88]--> unknown_B (7) <--[19..46]--> unknown_D (8) <--[0..1]--> unknown_E (10) <--[2..42]--> unknown_F (10) <--[9..128]--> unknown_G (11) <--[16..74]--> unknown_H (16) <--[9..54]--> unknown_I (8) <--[8..29]--> unknown_J (13) <--[8..42]--> unknown_K (15) <--[1..3]--> unknown_L (12) <--[6..15]--> unknown_M (13) <----
# human version. Use default transition matrix.
# Looks like ../data/chr4.103M.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 = 60001, name = chr4) -----
#
# Predicted genes for sequence number 1 on both strands
# start gene g1
chr4 AUGUSTUS gene 1070225 1119477 1 - . ID=g1
chr4 AUGUSTUS transcript 1070225 1119477 . - . ID=g1.t1;Parent=g1
chr4 AUGUSTUS stop_codon 1070225 1070227 . - 0 Parent=g1.t1
chr4 AUGUSTUS CDS 1070225 1070566 . - 0 ID=g1.t1.cds;Parent=g1.t1
chr4 AUGUSTUS CDS 1072377 1072535 . - 0 ID=g1.t1.cds;Parent=g1.t1
chr4 AUGUSTUS CDS 1079458 1079616 . - 0 ID=g1.t1.cds;Parent=g1.t1
chr4 AUGUSTUS CDS 1079772 1080044 . - 0 ID=g1.t1.cds;Parent=g1.t1
chr4 AUGUSTUS CDS 1080168 1080482 . - 0 ID=g1.t1.cds;Parent=g1.t1
chr4 AUGUSTUS CDS 1081783 1081937 . - 2 ID=g1.t1.cds;Parent=g1.t1
chr4 AUGUSTUS CDS 1082244 1082409 . - 0 ID=g1.t1.cds;Parent=g1.t1
chr4 AUGUSTUS CDS 1082493 1082615 . - 0 ID=g1.t1.cds;Parent=g1.t1
chr4 AUGUSTUS CDS 1084295 1084414 . - 0 ID=g1.t1.cds;Parent=g1.t1
chr4 AUGUSTUS CDS 1095894 1096061 . - 0 ID=g1.t1.cds;Parent=g1.t1
chr4 AUGUSTUS CDS 1097118 1097206 . - 2 ID=g1.t1.cds;Parent=g1.t1
chr4 AUGUSTUS CDS 1098057 1098204 . - 0 ID=g1.t1.cds;Parent=g1.t1
chr4 AUGUSTUS CDS 1101469 1101627 . - 0 ID=g1.t1.cds;Parent=g1.t1
chr4 AUGUSTUS CDS 1102495 1102614 . - 0 ID=g1.t1.cds;Parent=g1.t1
chr4 AUGUSTUS CDS 1103920 1104049 . - 1 ID=g1.t1.cds;Parent=g1.t1
chr4 AUGUSTUS CDS 1104359 1104446 . - 2 ID=g1.t1.cds;Parent=g1.t1
chr4 AUGUSTUS CDS 1106968 1107019 . - 0 ID=g1.t1.cds;Parent=g1.t1
chr4 AUGUSTUS CDS 1115387 1115452 . - 0 ID=g1.t1.cds;Parent=g1.t1
chr4 AUGUSTUS CDS 1115532 1115599 . - 2 ID=g1.t1.cds;Parent=g1.t1
chr4 AUGUSTUS CDS 1115761 1115842 . - 0 ID=g1.t1.cds;Parent=g1.t1
chr4 AUGUSTUS CDS 1116272 1116391 . - 0 ID=g1.t1.cds;Parent=g1.t1
chr4 AUGUSTUS CDS 1117078 1117196 . - 2 ID=g1.t1.cds;Parent=g1.t1
chr4 AUGUSTUS CDS 1117321 1117410 . - 2 ID=g1.t1.cds;Parent=g1.t1
chr4 AUGUSTUS CDS 1117917 1118008 . - 1 ID=g1.t1.cds;Parent=g1.t1
chr4 AUGUSTUS CDS 1119422 1119477 . - 0 ID=g1.t1.cds;Parent=g1.t1
chr4 AUGUSTUS start_codon 1119475 1119477 . - 0 Parent=g1.t1
chr4 AUGUSTUS protein_match 1102591 1102614 3.08 - 0 ID=pp.g1.t1.unknown_M;Target=unknown_M 6 13;Target_start=316;
chr4 AUGUSTUS protein_match 1103920 1103934 2.19 - 0 ID=pp.g1.t1.unknown_M;Target=unknown_M 1 5;Target_start=316;
chr4 AUGUSTUS protein_match 1103953 1103988 4.85 - 0 ID=pp.g1.t1.unknown_L;Target=unknown_L 1 12;Target_start=298;
chr4 AUGUSTUS protein_match 1103992 1104036 8.38 - 0 ID=pp.g1.t1.unknown_K;Target=unknown_K 1 15;Target_start=282;
chr4 AUGUSTUS protein_match 1104376 1104414 3.96 - 0 ID=pp.g1.t1.unknown_J;Target=unknown_J 1 13;Target_start=259;
chr4 AUGUSTUS protein_match 1106993 1107016 9.22 - 0 ID=pp.g1.t1.unknown_I;Target=unknown_I 1 8;Target_start=232;
chr4 AUGUSTUS protein_match 1115568 1115599 3.74 - 2 ID=pp.g1.t1.unknown_H;Target=unknown_H 6 16;Target_start=181;
chr4 AUGUSTUS protein_match 1115761 1115776 1.96 - 0 ID=pp.g1.t1.unknown_H;Target=unknown_H 1 6;Target_start=181;
chr4 AUGUSTUS protein_match 1116320 1116352 7.34 - 0 ID=pp.g1.t1.unknown_G;Target=unknown_G 1 11;Target_start=132;
chr4 AUGUSTUS protein_match 1117093 1117122 5.11 - 0 ID=pp.g1.t1.unknown_F;Target=unknown_F 1 10;Target_start=104;
chr4 AUGUSTUS protein_match 1117147 1117176 9.44 - 0 ID=pp.g1.t1.unknown_E;Target=unknown_E 1 10;Target_start=86;
chr4 AUGUSTUS protein_match 1117177 1117196 9.28 - 2 ID=pp.g1.t1.unknown_D;Target=unknown_D 2 8;Target_start=78;
chr4 AUGUSTUS protein_match 1117321 1117324 13.8 - 0 ID=pp.g1.t1.unknown_D;Target=unknown_D 1 2;Target_start=78;
chr4 AUGUSTUS protein_match 1117400 1117410 7.4 - 2 ID=pp.g1.t1.unknown_B;Target=unknown_B 4 7;Target_start=46;
chr4 AUGUSTUS protein_match 1117917 1117926 5.9 - 0 ID=pp.g1.t1.unknown_B;Target=unknown_B 1 4;Target_start=46;
chr4 AUGUSTUS protein_match 1118005 1118008 7.54 - 1 ID=pp.g1.t1.unknown_A;Target=unknown_A 8 9;Target_start=11;
chr4 AUGUSTUS protein_match 1119422 1119444 6.1 - 0 ID=pp.g1.t1.unknown_A;Target=unknown_A 1 8;Target_start=11;
chr4 AUGUSTUS interblock_region 1070225 1070566 . - 0 ID=pp.g1.t1.iBR12
chr4 AUGUSTUS interblock_region 1072377 1072535 . - 0 ID=pp.g1.t1.iBR12
chr4 AUGUSTUS interblock_region 1079458 1079616 . - 0 ID=pp.g1.t1.iBR12
chr4 AUGUSTUS interblock_region 1079772 1080044 . - 0 ID=pp.g1.t1.iBR12
chr4 AUGUSTUS interblock_region 1080168 1080482 . - 0 ID=pp.g1.t1.iBR12
chr4 AUGUSTUS interblock_region 1081783 1081937 . - 2 ID=pp.g1.t1.iBR12
chr4 AUGUSTUS interblock_region 1082244 1082409 . - 0 ID=pp.g1.t1.iBR12
chr4 AUGUSTUS interblock_region 1082493 1082615 . - 0 ID=pp.g1.t1.iBR12
chr4 AUGUSTUS interblock_region 1084295 1084414 . - 0 ID=pp.g1.t1.iBR12
chr4 AUGUSTUS interblock_region 1095894 1096061 . - 0 ID=pp.g1.t1.iBR12
chr4 AUGUSTUS interblock_region 1097118 1097206 . - 2 ID=pp.g1.t1.iBR12
chr4 AUGUSTUS interblock_region 1098057 1098204 . - 0 ID=pp.g1.t1.iBR12
chr4 AUGUSTUS interblock_region 1101469 1101627 . - 0 ID=pp.g1.t1.iBR12
chr4 AUGUSTUS interblock_region 1102495 1102590 . - 0 ID=pp.g1.t1.iBR12
chr4 AUGUSTUS interblock_region 1103935 1103952 . - 0 ID=pp.g1.t1.iBR11
chr4 AUGUSTUS interblock_region 1103989 1103991 . - 0 ID=pp.g1.t1.iBR10
chr4 AUGUSTUS interblock_region 1104037 1104049 . - 1 ID=pp.g1.t1.iBR9
chr4 AUGUSTUS interblock_region 1104359 1104375 . - 0 ID=pp.g1.t1.iBR9
chr4 AUGUSTUS interblock_region 1104415 1104446 . - 2 ID=pp.g1.t1.iBR8
chr4 AUGUSTUS interblock_region 1106968 1106992 . - 0 ID=pp.g1.t1.iBR8
chr4 AUGUSTUS interblock_region 1107017 1107019 . - 0 ID=pp.g1.t1.iBR7
chr4 AUGUSTUS interblock_region 1115387 1115452 . - 0 ID=pp.g1.t1.iBR7
chr4 AUGUSTUS interblock_region 1115532 1115567 . - 0 ID=pp.g1.t1.iBR7
chr4 AUGUSTUS interblock_region 1115777 1115842 . - 0 ID=pp.g1.t1.iBR6
chr4 AUGUSTUS interblock_region 1116272 1116319 . - 0 ID=pp.g1.t1.iBR6
chr4 AUGUSTUS interblock_region 1116353 1116391 . - 0 ID=pp.g1.t1.iBR5
chr4 AUGUSTUS interblock_region 1117078 1117092 . - 0 ID=pp.g1.t1.iBR5
chr4 AUGUSTUS interblock_region 1117123 1117146 . - 0 ID=pp.g1.t1.iBR4
chr4 AUGUSTUS interblock_region 1117325 1117399 . - 0 ID=pp.g1.t1.iBR2
chr4 AUGUSTUS interblock_region 1117927 1118004 . - 0 ID=pp.g1.t1.iBR1
chr4 AUGUSTUS interblock_region 1119445 1119477 . - 0 ID=pp.g1.t1.iBR0
# protein sequence = [MAEEGAVAVCVRVRPLNSREESLGETAQVYWKTDNNVIYQVDGSKSFNFDRVFHGNETTKNVYEEIAAPIIDSAIQGY
# NGTIFAYGQTASGKTYTMMGSEDHLGVIPRAIHDIFQKIKKFPDREFLLRVSYMEIYNETITDLLCGTQKMKPLIIREDVNRNVYVADLTEEVVYTSE
# MALKWITKGEKSRHYGETKMNQRSSRSHTIFRMILESREKGEPSNCEGSVKVSHLNLVDLAGSERAAQTGAAGVRLKEGCNINRSLFILGQVIKKLSD
# GQVGGFINYRDSKLTRILQNSLGGNAKTRIICTITPVSFDETLTALQFASTAKYMKNTPYVNEVSTDEALLKRYRKEIMDLKKQLEEVSLETRAQAME
# KDQLAQLLEEKDLLQKVQNEKIENLTRMLVTSSSLTLQQELKAKRKRRVTWCLGKINKMKNSNYADQFNIPTNITTKTHKLSINLLREIDESVCSESD
# VFSNTLDTLSEIEWNPATKLLNQENIESELNSLRADYDNLVLDYEQLRTEKEEMELKLKEKNDLDEFEALERKTKKDQENELSSKVELLREKEDQIKK
# LQEYIDSQKLENIKMDLSYSLESIEDPKQMKQTLFDAETVALDAKRESAFLRSENLELKEKMKELATTYKQMENDIQLYQSQLEAKKKMQVDLEKELQ
# SAFNEITKLTSLIDGKVPKDLLCNLELEGKITDLQKELNKEVEENEALREEVILLSELKSLPSEVERLRKEIQDKSEELHIITSEKDKLFSEVVHKES
# RVQGLLEEIGKTKDDLATTQSNYKSTDQEFQNFKTLHMDFEQKYKMVLEENERMNQEIVNLSKEAQKFDSSLGALKTELSYKTQELQEKTREVQERLN
# EMEQLKEQLENRDSTLQTVEREKTLITEKLQQTLEEVKTLTQEKDDLKQLQESLQIERDQLKSDIHDTVNMNIDTQEQLRNALESLKQHQETINTLKS
# KISEEVSRNLHMEENTGETKDEFQQKTIENQEELRLLGDELKKQQEIVAQEKNHAIKKEGELSRTCDRLAEVEEKLKEKSQQLQEKQQQLLNVQEEMS
# EMQKKINEIENLKNELKNKELTLEHMETERLELAQKLNENYEEVKSITKERKVLKELQKSFETERDHLRGYIREIEATVSYTLFLHLLSVSFKI]
# sequence of block unknown_M 316 [LTALQFASTAKYM] 329
# sequence of block unknown_L 298 [NAKTRIICTITP] 310
# sequence of block unknown_K 282 [YRDSKLTRILQNSLG] 297
# sequence of block unknown_J 259 [RSLFILGQVIKKL] 272
# sequence of block unknown_I 232 [LVDLAGSE] 240
# sequence of block unknown_H 181 [ITKGEKSRHYGETKMN] 197
# sequence of block unknown_G 132 [EIYNETITDLL] 143
# sequence of block unknown_F 104 [VIPRAIHDIF] 114
# sequence of block unknown_E 86 [QTASGKTYTM] 96
# sequence of block unknown_D 78 [NGTIFAYG] 86
# sequence of block unknown_B 46 [FNFDRVF] 53
# sequence of block unknown_A 11 [RVRPLNSRE] 20
# end gene g1
###
# command line:
# augustus --optCfgFile=../data/ppx.cfg --predictionStart=1070000 --predictionEnd=1130000 --proteinprofile=../results/PF00225_seed.prfl ../data/chr4.103M.fa
|
