# 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 # --[0..66]--> unknown_A (21) <--[10..131]--> unknown_C (18) <--[1..19]--> unknown_D (33) <--[0..4]--> unknown_E (15) <--[8..25]--> unknown_F (17) <--[2..42]--> unknown_G (30) <--[0..690]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig2068920180911_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 = 4918, name = Contig20689) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig20689 AUGUSTUS gene 1 4725 0.01 - . g1 Contig20689 AUGUSTUS transcript 1 4725 0.01 - . g1.t1 Contig20689 AUGUSTUS tts 1 1 . - . transcript_id "g1.t1"; gene_id "g1"; Contig20689 AUGUSTUS exon 1 803 . - . transcript_id "g1.t1"; gene_id "g1"; Contig20689 AUGUSTUS stop_codon 570 572 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig20689 AUGUSTUS intron 804 2934 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig20689 AUGUSTUS intron 3210 3675 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig20689 AUGUSTUS intron 3751 4097 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig20689 AUGUSTUS intron 4115 4254 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig20689 AUGUSTUS intron 4267 4363 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig20689 AUGUSTUS intron 4389 4684 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig20689 AUGUSTUS CDS 570 803 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig20689 AUGUSTUS CDS 2935 3209 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig20689 AUGUSTUS exon 2935 3209 . - . transcript_id "g1.t1"; gene_id "g1"; Contig20689 AUGUSTUS CDS 3676 3750 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig20689 AUGUSTUS exon 3676 3750 . - . transcript_id "g1.t1"; gene_id "g1"; Contig20689 AUGUSTUS CDS 4098 4114 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig20689 AUGUSTUS exon 4098 4114 . - . transcript_id "g1.t1"; gene_id "g1"; Contig20689 AUGUSTUS CDS 4255 4266 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig20689 AUGUSTUS exon 4255 4266 . - . transcript_id "g1.t1"; gene_id "g1"; Contig20689 AUGUSTUS CDS 4364 4388 0.01 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig20689 AUGUSTUS exon 4364 4388 . - . transcript_id "g1.t1"; gene_id "g1"; Contig20689 AUGUSTUS CDS 4685 4691 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig20689 AUGUSTUS exon 4685 4725 . - . transcript_id "g1.t1"; gene_id "g1"; Contig20689 AUGUSTUS start_codon 4689 4691 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig20689 AUGUSTUS tss 4725 4725 . - . transcript_id "g1.t1"; gene_id "g1"; Contig20689 AUGUSTUS protein_match 645 734 3.67 - 0 target "unknown_G[1..30]"; target_start 160; transcript_id "g1.t1"; gene_id "g1"; Contig20689 AUGUSTUS protein_match 756 803 4.33 - 0 target "unknown_F[2..17]"; target_start 136; transcript_id "g1.t1"; gene_id "g1"; Contig20689 AUGUSTUS protein_match 2935 2937 4.05 - 0 target "unknown_F[1..1]"; target_start 136; transcript_id "g1.t1"; gene_id "g1"; Contig20689 AUGUSTUS protein_match 2968 3012 2.84 - 0 target "unknown_E[1..15]"; target_start 111; transcript_id "g1.t1"; gene_id "g1"; Contig20689 AUGUSTUS protein_match 3013 3111 4.09 - 0 target "unknown_D[1..33]"; target_start 78; transcript_id "g1.t1"; gene_id "g1"; Contig20689 AUGUSTUS protein_match 3127 3180 4.8 - 0 target "unknown_C[1..18]"; target_start 55; transcript_id "g1.t1"; gene_id "g1"; Contig20689 AUGUSTUS protein_match 3734 3750 1.25 - 2 target "unknown_A[16..21]"; target_start 5; transcript_id "g1.t1"; gene_id "g1"; Contig20689 AUGUSTUS protein_match 4098 4114 1.3 - 1 target "unknown_A[10..16]"; target_start 5; transcript_id "g1.t1"; gene_id "g1"; Contig20689 AUGUSTUS protein_match 4255 4266 1 - 1 target "unknown_A[6..10]"; target_start 5; transcript_id "g1.t1"; gene_id "g1"; Contig20689 AUGUSTUS protein_match 4364 4380 1.12 - 0 target "unknown_A[1..6]"; target_start 5; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgaaagcacttctcaacttccttggttgccaacctgtgttaaaagaggaaaagctcattgtatcgagatacatgtata # gtaacgcgtgtatcgagatacgtatcgtaagctttgtgtatcgtcccacccctactggctaccttgatagcagttcagagtctgaaaacttacaaccc # ggtaccaaactggagctgccatactggatggcaagggcactgtgcagcaggaagcgacacattataagtgttgaattgccaaagcagtacaaggaggg # gtatagagaaattttctcggcagacccaactgtggtagatttacacaaacttggaccctacttttataactatgggaaccagctcctcagatttgaac # ttccagaaacacctgatgttgccaagacgctgttacagacttttcaaggacgtttaagaaaaataatggacagctcacaaaattcattcaatgaagat # tcctccagacttgtagaaaagcttgatgaatctgagagaattttattcagagagggacagaaagctctaaatgattttcaatgttgggaaaccaggaa # aactgaaaagctgaccacctcagaaatggtgaaacatcacaggaagagaaaacgagtggttctggaggaatcttga] # protein sequence = [MKALLNFLGCQPVLKEEKLIVSRYMYSNACIEIRIVSFVYRPTPTGYLDSSSESENLQPGTKLELPYWMARALCSRKR # HIISVELPKQYKEGYREIFSADPTVVDLHKLGPYFYNYGNQLLRFELPETPDVAKTLLQTFQGRLRKIMDSSQNSFNEDSSRLVEKLDESERILFREG # QKALNDFQCWETRKTEKLTTSEMVKHHRKRKRVVLEES] # sequence of block unknown_G 160 [LVEKLDESERILFREGQKALNDFQCWETRK] 190 # sequence of block unknown_F 136 [QTFQGRLRKIMDSSQNS] 153 # sequence of block unknown_E 111 [YFYNYGNQLLRFELP] 126 # sequence of block unknown_D 78 [HIISVELPKQYKEGYREIFSADPTVVDLHKLGP] 111 # sequence of block unknown_C 55 [NLQPGTKLELPYWMARAL] 73 # sequence of block unknown_A 5 [NFLGCQPVLKEEKLIVSRYMY] 26 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370XFG.prfl --predictionStart=0 --predictionEnd=23210 --species=fly ./tmp/Contig2068920180911_busco_2432604931_.temp