# 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 # --[6..195]--> unknown_B (18) <--[7..19]--> unknown_D (14) <--[0..1]--> unknown_E (13) <--[1..65]--> unknown_F (63) <--[0..101]--> unknown_G (25) <--[2..8]--> unknown_H (15) <--[2..42]--> unknown_I (21) <--[4..46]--> unknown_J (22) <--[0..3]--> unknown_K (27) <--[8..214]--> unknown_L (27) <--[0..88]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig17027220180911_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 = 9437, name = Contig170272) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig170272 AUGUSTUS gene 296 7420 0.01 + . g1 Contig170272 AUGUSTUS transcript 296 7420 0.01 + . g1.t1 Contig170272 AUGUSTUS tss 296 296 . + . transcript_id "g1.t1"; gene_id "g1"; Contig170272 AUGUSTUS exon 296 413 . + . transcript_id "g1.t1"; gene_id "g1"; Contig170272 AUGUSTUS exon 2750 3160 . + . transcript_id "g1.t1"; gene_id "g1"; Contig170272 AUGUSTUS start_codon 2836 2838 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig170272 AUGUSTUS intron 3161 4830 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig170272 AUGUSTUS intron 5098 5452 0.04 + . transcript_id "g1.t1"; gene_id "g1"; Contig170272 AUGUSTUS CDS 2836 3160 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig170272 AUGUSTUS CDS 4831 5097 0.02 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig170272 AUGUSTUS exon 4831 5097 . + . transcript_id "g1.t1"; gene_id "g1"; Contig170272 AUGUSTUS CDS 5453 5910 0.03 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig170272 AUGUSTUS exon 5453 7420 . + . transcript_id "g1.t1"; gene_id "g1"; Contig170272 AUGUSTUS stop_codon 5908 5910 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig170272 AUGUSTUS tts 7420 7420 . + . transcript_id "g1.t1"; gene_id "g1"; Contig170272 AUGUSTUS protein_match 2857 2910 4.46 + 0 target "unknown_B[1..18]"; target_start 7; transcript_id "g1.t1"; gene_id "g1"; Contig170272 AUGUSTUS protein_match 2932 2973 6.1 + 0 target "unknown_D[1..14]"; target_start 32; transcript_id "g1.t1"; gene_id "g1"; Contig170272 AUGUSTUS protein_match 2974 3012 3.04 + 0 target "unknown_E[1..13]"; target_start 46; transcript_id "g1.t1"; gene_id "g1"; Contig170272 AUGUSTUS protein_match 3016 3160 5.81 + 0 target "unknown_F[1..49]"; target_start 60; transcript_id "g1.t1"; gene_id "g1"; Contig170272 AUGUSTUS protein_match 4831 4874 5.89 + 2 target "unknown_F[49..63]"; target_start 60; transcript_id "g1.t1"; gene_id "g1"; Contig170272 AUGUSTUS protein_match 4884 4958 5.89 + 0 target "unknown_G[1..25]"; target_start 126; transcript_id "g1.t1"; gene_id "g1"; Contig170272 AUGUSTUS protein_match 4968 5012 4.59 + 0 target "unknown_H[1..15]"; target_start 154; transcript_id "g1.t1"; gene_id "g1"; Contig170272 AUGUSTUS protein_match 5019 5081 6.63 + 0 target "unknown_I[1..21]"; target_start 171; transcript_id "g1.t1"; gene_id "g1"; Contig170272 AUGUSTUS protein_match 5097 5097 1 + 0 target "unknown_J[1..1]"; target_start 197; transcript_id "g1.t1"; gene_id "g1"; Contig170272 AUGUSTUS protein_match 5453 5517 9.14 + 2 target "unknown_J[1..22]"; target_start 197; transcript_id "g1.t1"; gene_id "g1"; Contig170272 AUGUSTUS protein_match 5521 5601 3.15 + 0 target "unknown_K[1..27]"; target_start 220; transcript_id "g1.t1"; gene_id "g1"; Contig170272 AUGUSTUS protein_match 5824 5904 3.76 + 0 target "unknown_L[1..27]"; target_start 321; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgagtttcaacaaataccatgaaaaagtgaaagaaaatgacactgtcatactctatttaggatatgacaatatgcatg # ccattaagattaaaagaggctcggtttttcaaacgaaatatggggccttacgacacagcgacatcattggaacgacgtacggaaatcgagtccagtgt # ccaaaggggtacctgtatattctgtaccctactcccgagttgtggacgtcaaatttaccacatagaacacaaattctctactcaacagatattagtgt # ggtttcataccagcttgatctcaagcctggggcagttgtagttgaatcaggtacaggaagtgcatccctgtcgcattccatcattaggtccattttgc # caaatggtcatctctatacctttgaatttcacaaagaaagagcacagaaagcagaggaagaactgacggaccatggactctctgactatgtcacagta # actcataaagatgtctgtaagtttggctttgagctggaggatgttgctgacgcagtgttcctagatttaccagttccttgggatgctctaccaagtgc # aaagaaagctttgaaaaagataggaggaaggatctgttccttttcaccgtgcatcgaacaagtccagaaaacctgtgcatgcttggcagagttaggat # ttgaagaaatttcaacaatggagtgtctcgtcagaaactatgatgtgagaacaattaatttgcctaaccctgaattctcccgagaaaattcgaagtca # ctgcctcagcagaaaggtacaaagttggaacaggaggacatggacacggactcacctagcgagtctgtagagaaatcctcacaatgtgggaaatctgg # tgacaagaaaacaacaatgtgcaactctaaagacaaaggtcaaattgctgaggtcttagatacccctgcctgggactatattggtaaaaaaacagctg # caaacttttctttcaaatctggggtttccgttggaaaaatgccaggacacaccggatatttgacttttgcaacactttatccattgtag] # protein sequence = [MSFNKYHEKVKENDTVILYLGYDNMHAIKIKRGSVFQTKYGALRHSDIIGTTYGNRVQCPKGYLYILYPTPELWTSNL # PHRTQILYSTDISVVSYQLDLKPGAVVVESGTGSASLSHSIIRSILPNGHLYTFEFHKERAQKAEEELTDHGLSDYVTVTHKDVCKFGFELEDVADAV # FLDLPVPWDALPSAKKALKKIGGRICSFSPCIEQVQKTCACLAELGFEEISTMECLVRNYDVRTINLPNPEFSRENSKSLPQQKGTKLEQEDMDTDSP # SESVEKSSQCGKSGDKKTTMCNSKDKGQIAEVLDTPAWDYIGKKTAANFSFKSGVSVGKMPGHTGYLTFATLYPL] # sequence of block unknown_B 7 [EKVKENDTVILYLGYDNM] 25 # sequence of block unknown_D 32 [GSVFQTKYGALRHS] 46 # sequence of block unknown_E 46 [DIIGTTYGNRVQC] 59 # sequence of block unknown_F 60 [KGYLYILYPTPELWTSNLPHRTQILYSTDISVVSYQLDLKPGAVVVESGTGSASLSHSIIRSI] 123 # sequence of block unknown_G 126 [GHLYTFEFHKERAQKAEEELTDHGL] 151 # sequence of block unknown_H 154 [VTVTHKDVCKFGFEL] 169 # sequence of block unknown_I 171 [VADAVFLDLPVPWDALPSAKK] 192 # sequence of block unknown_J 197 [GGRICSFSPCIEQVQKTCACLA] 219 # sequence of block unknown_K 220 [LGFEEISTMECLVRNYDVRTINLPNPE] 247 # sequence of block unknown_L 321 [NFSFKSGVSVGKMPGHTGYLTFATLYP] 348 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370OHP.prfl --predictionStart=0 --predictionEnd=25577 --species=fly ./tmp/Contig17027220180911_busco_2432604931_.temp