# 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 using config directory /augustus/config/ ... # Using protein profile unknown # --[7..84]--> unknown_A (21) <--[0..2]--> unknown_B (40) <--[0..17]--> unknown_C (24) <--[0..44]--> unknown_D (19) <--[0..39]--> unknown_E (12) <--[0..28]--> unknown_F (46) <--[1..4]--> unknown_G (12) <--[0..1]--> unknown_H (44) <--[1..27]--> unknown_I (18) <--[0..7]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig7820180911_busco_2432604931_.temp 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 = 25986, name = Contig78) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig78 AUGUSTUS gene 1 21775 0.01 - . g1 Contig78 AUGUSTUS transcript 1 21775 0.01 - . g1.t1 Contig78 AUGUSTUS tts 1 1 . - . transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS exon 1 43 . - . transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS stop_codon 6 8 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS intron 44 100 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS intron 111 380 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS intron 400 724 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS intron 753 913 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS intron 1078 1987 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS intron 2077 3244 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS intron 3352 3688 0.06 - . transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS intron 3776 3832 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS intron 3950 5868 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS intron 6019 21450 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS CDS 6 43 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS CDS 101 110 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS exon 101 110 . - . transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS CDS 381 399 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS exon 381 399 . - . transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS CDS 725 752 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS exon 725 752 . - . transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS CDS 914 1077 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS exon 914 1077 . - . transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS CDS 1988 2076 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS exon 1988 2076 . - . transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS CDS 3245 3351 0.05 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS exon 3245 3351 . - . transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS CDS 3689 3775 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS exon 3689 3775 . - . transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS CDS 3833 3949 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS exon 3833 3949 . - . transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS CDS 5869 6018 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS exon 5869 6018 . - . transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS CDS 21451 21637 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS exon 21451 21775 . - . transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS start_codon 21635 21637 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS tss 21775 21775 . - . transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS protein_match 27 43 1.28 - 2 target "unknown_I[13..18]"; target_start 307; transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS protein_match 101 110 2.29 - 0 target "unknown_I[10..13]"; target_start 307; transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS protein_match 381 399 1.65 - 1 target "unknown_I[3..9]"; target_start 307; transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS protein_match 725 732 0.13 - 0 target "unknown_I[1..3]"; target_start 307; transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS protein_match 924 1055 3 - 0 target "unknown_H[1..44]"; target_start 253; transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS protein_match 1059 1077 6.46 - 1 target "unknown_G[6..12]"; target_start 240; transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS protein_match 1988 2004 2.03 - 0 target "unknown_G[1..6]"; target_start 240; transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS protein_match 2011 2076 8.87 - 0 target "unknown_F[25..46]"; target_start 192; transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS protein_match 3245 3316 8.31 - 0 target "unknown_F[1..24]"; target_start 192; transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS protein_match 3317 3351 5.67 - 2 target "unknown_E[1..12]"; target_start 180; transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS protein_match 3689 3689 1 - 0 target "unknown_E[1..1]"; target_start 180; transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS protein_match 3717 3773 6.5 - 0 target "unknown_D[1..19]"; target_start 152; transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS protein_match 3915 3949 5.83 - 2 target "unknown_C[13..24]"; target_start 100; transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS protein_match 5869 5905 6.58 - 0 target "unknown_C[1..13]"; target_start 100; transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS protein_match 5906 6018 7.54 - 2 target "unknown_B[3..40]"; target_start 60; transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS protein_match 21451 21457 1.5 - 0 target "unknown_B[1..3]"; target_start 60; transcript_id "g1.t1"; gene_id "g1"; Contig78 AUGUSTUS protein_match 21458 21520 3.75 - 0 target "unknown_A[1..21]"; target_start 39; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atggcagctgccttgaaagccggtggtggtgggttctgccgtcaaagggaaaaaccaatcacaagcattatttttaggt # tattggccacaagtacagcagcacgtgaggataaaagaacaaaaagggaaactaaagacactcattttggatttgaaactgttgcagaagatgagaaa # gaagacagagtgtatgaagtttttaagaatgttgccagcaaatatgacctaatgaatgacacaatgagccttggcatacacagactatggaaagacca # tttcatacacaaactggccccaatagcagggaccaaattattagacgttgcaggaggtacaggtgatattgcatttcgttttctccaatacacacaat # cacaaactgatgaagcagttgtgacagatgaacattttactattcctacaaacataacaacaggagcctttttcattcctaatacttctcatgtaaca # gtgtgtgatattaaccaagaaatgctaagtgtcggaaaatctcgtgcagaagaagcaggaataacttcaggcatcagctgggttcaaggaaatgcaga # gtgtttaccatttgaagataataattttgatgcttacacaattgcttatggaattcgcaactgtacccacatcgacaaagtcttaacagaggcacaca # gagtgcttaagcctggaggacgatttatgtgtttggaatttagtcaagttaataatttagttttacgtaggttgtatgactcctattcatttgaagtg # atacctgtaatggggcaggtgcttgctaaggactggaaatcttaccagtatttagtggaaagcataaggcagtttccaaatcaggtatcttcttcttt # tttttttattcttttttttttttttttttttttttttttgctcatccatcatctgctgtttaactctgaccttagccttgctgttgtattgattagat # ctatttgcaaaatattagggctgcgtatcggatga] # protein sequence = [MAAALKAGGGGFCRQREKPITSIIFRLLATSTAAREDKRTKRETKDTHFGFETVAEDEKEDRVYEVFKNVASKYDLMN # DTMSLGIHRLWKDHFIHKLAPIAGTKLLDVAGGTGDIAFRFLQYTQSQTDEAVVTDEHFTIPTNITTGAFFIPNTSHVTVCDINQEMLSVGKSRAEEA # GITSGISWVQGNAECLPFEDNNFDAYTIAYGIRNCTHIDKVLTEAHRVLKPGGRFMCLEFSQVNNLVLRRLYDSYSFEVIPVMGQVLAKDWKSYQYLV # ESIRQFPNQVSSSFFFILFFFFFFFFLLIHHLLFNSDLSLAVVLIRSICKILGLRIG] # sequence of block unknown_I 307 [FNSDLSLAVVLIRSICKI] 325 # sequence of block unknown_H 253 [EVIPVMGQVLAKDWKSYQYLVESIRQFPNQVSSSFFFILFFFFF] 297 # sequence of block unknown_G 240 [NLVLRRLYDSYS] 252 # sequence of block unknown_F 192 [PFEDNNFDAYTIAYGIRNCTHIDKVLTEAHRVLKPGGRFMCLEFSQ] 238 # sequence of block unknown_E 180 [GISWVQGNAECL] 192 # sequence of block unknown_D 152 [TSHVTVCDINQEMLSVGKS] 171 # sequence of block unknown_C 100 [AGTKLLDVAGGTGDIAFRFLQYTQ] 124 # sequence of block unknown_B 60 [DRVYEVFKNVASKYDLMNDTMSLGIHRLWKDHFIHKLAPI] 100 # sequence of block unknown_A 39 [TKRETKDTHFGFETVAEDEKE] 60 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370MMK.prfl --predictionStart=0 --predictionEnd=25986 --species=fly ./tmp/Contig7820180911_busco_2432604931_.temp