# 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..1271]--> unknown_A (22) <--[1..7]--> unknown_B (19) <--[4..64]--> unknown_C (10) <--[1..33]--> unknown_D (49) <--[1..28]--> unknown_E (27) <--[5..34]--> unknown_F (15) <--[0..1]--> unknown_G (19) <--[0..355]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig2907120180911_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 = 37268, name = Contig29071) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig29071 AUGUSTUS gene 1817 14218 0.01 + . g1 Contig29071 AUGUSTUS transcript 1817 14218 0.01 + . g1.t1 Contig29071 AUGUSTUS exon 1817 1840 . + . transcript_id "g1.t1"; gene_id "g1"; Contig29071 AUGUSTUS start_codon 1824 1826 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig29071 AUGUSTUS intron 1841 12815 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig29071 AUGUSTUS CDS 1824 1840 0.03 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig29071 AUGUSTUS CDS 12816 13044 0.76 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig29071 AUGUSTUS exon 12816 13045 . + . transcript_id "g1.t1"; gene_id "g1"; Contig29071 AUGUSTUS stop_codon 13042 13044 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig29071 AUGUSTUS exon 13479 14218 . + . transcript_id "g1.t1"; gene_id "g1"; Contig29071 AUGUSTUS tts 14218 14218 . + . transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgtcaaaggttcaaagcaacagagtgacgagagacggtgcactggagctggcgaaggtactgaaggagaatacagcca # tcgagatcctggacctcggctacaacaggctggaggatgatggggncaaggtgttgaaggagaataccgccatcgagatcctggatctcggctacaac # aggctggaggatgatggggcgtgtcacattgctgaggctctcaaaactctcaatacaaatctccaatag] # protein sequence = [MSKVQSNRVTRDGALELAKVLKENTAIEILDLGYNRLEDDGXKVLKENTAIEILDLGYNRLEDDGACHIAEALKTLNT # NLQ] # end gene g1 ### # start gene g2 Contig29071 AUGUSTUS gene 15197 23095 0.01 - . g2 Contig29071 AUGUSTUS transcript 15197 23095 0.01 - . g2.t1 Contig29071 AUGUSTUS tts 15197 15197 . - . transcript_id "g2.t1"; gene_id "g2"; Contig29071 AUGUSTUS exon 15197 15306 . - . transcript_id "g2.t1"; gene_id "g2"; Contig29071 AUGUSTUS stop_codon 15239 15241 . - 0 transcript_id "g2.t1"; gene_id "g2"; Contig29071 AUGUSTUS intron 15307 16265 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig29071 AUGUSTUS intron 16435 17139 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig29071 AUGUSTUS intron 17269 17498 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig29071 AUGUSTUS intron 17595 18650 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig29071 AUGUSTUS intron 18864 22429 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig29071 AUGUSTUS CDS 15239 15306 0.01 - 2 transcript_id "g2.t1"; gene_id "g2"; Contig29071 AUGUSTUS CDS 16266 16434 0.01 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig29071 AUGUSTUS exon 16266 16434 . - . transcript_id "g2.t1"; gene_id "g2"; Contig29071 AUGUSTUS CDS 17140 17268 0.01 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig29071 AUGUSTUS exon 17140 17268 . - . transcript_id "g2.t1"; gene_id "g2"; Contig29071 AUGUSTUS CDS 17499 17594 0.02 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig29071 AUGUSTUS exon 17499 17594 . - . transcript_id "g2.t1"; gene_id "g2"; Contig29071 AUGUSTUS CDS 18651 18863 0.01 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig29071 AUGUSTUS exon 18651 18863 . - . transcript_id "g2.t1"; gene_id "g2"; Contig29071 AUGUSTUS CDS 22430 22498 0.01 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig29071 AUGUSTUS exon 22430 22518 . - . transcript_id "g2.t1"; gene_id "g2"; Contig29071 AUGUSTUS start_codon 22496 22498 . - 0 transcript_id "g2.t1"; gene_id "g2"; Contig29071 AUGUSTUS exon 23066 23095 . - . transcript_id "g2.t1"; gene_id "g2"; Contig29071 AUGUSTUS tss 23095 23095 . - . transcript_id "g2.t1"; gene_id "g2"; Contig29071 AUGUSTUS protein_match 15245 15301 3.47 - 0 target "unknown_G[1..19]"; target_start 227; transcript_id "g2.t1"; gene_id "g2"; Contig29071 AUGUSTUS protein_match 15305 15306 1 - 2 target "unknown_F[15..15]"; target_start 211; transcript_id "g2.t1"; gene_id "g2"; Contig29071 AUGUSTUS protein_match 16266 16308 8.69 - 0 target "unknown_F[1..15]"; target_start 211; transcript_id "g2.t1"; gene_id "g2"; Contig29071 AUGUSTUS protein_match 16324 16404 7.67 - 0 target "unknown_E[1..27]"; target_start 179; transcript_id "g2.t1"; gene_id "g2"; Contig29071 AUGUSTUS protein_match 16408 16434 9.91 - 0 target "unknown_D[41..49]"; target_start 129; transcript_id "g2.t1"; gene_id "g2"; Contig29071 AUGUSTUS protein_match 17140 17259 7.64 - 0 target "unknown_D[1..40]"; target_start 129; transcript_id "g2.t1"; gene_id "g2"; Contig29071 AUGUSTUS protein_match 17499 17528 5.36 - 0 target "unknown_C[1..10]"; target_start 116; transcript_id "g2.t1"; gene_id "g2"; Contig29071 AUGUSTUS protein_match 17541 17594 4.94 - 0 target "unknown_B[2..19]"; target_start 93; transcript_id "g2.t1"; gene_id "g2"; Contig29071 AUGUSTUS protein_match 18651 18653 2.99 - 0 target "unknown_B[1..1]"; target_start 93; transcript_id "g2.t1"; gene_id "g2"; Contig29071 AUGUSTUS protein_match 18660 18725 5.76 - 0 target "unknown_A[1..22]"; target_start 69; transcript_id "g2.t1"; gene_id "g2"; # coding sequence = [atgacgccatgttacaaagttcggctgctttatttgaatttgactataccagaagtggatacgctgaagtcaacaatac # ctcccagttctgcttgcatagcatctgcaaccaacgaggtcatttttgtttctgtcggaagtgaacttctgaacccggttatactttcactttcggtt # tacctgatgagtgggacagaaacgaggaggattttagttgggtgcactggaagtgttgcatctattaaaatacctttattagtgcaagagcttcaatg # tgacaaggtcgacatcaaagtggtggctactgagcatgcacttcacttttttgacaaggactcgcttcaagtaccagtcctgacagacagagatgaat # gggagaattggaaaagtgtggcagatccagttcttcatattgagttaagaagatgggcagacatcttagtgatagccccactagactgtaacacactg # gccaagatggctaatggcatctgtgataacttgctgacttgtatagtgagagcctgggatctaagtaagccattatactttgctccagccatgaacac # atacatgtggcaacacccgatcacagcacaacagatagagacactaaaaagctataactataaagaaatcccctgtatagagaagaagttggcttgtg # gagacacagggtttggagcaatggcggaagtgtgtaccattgtaagcagtgttaaggaggctttagacttgacatga] # protein sequence = [MTPCYKVRLLYLNLTIPEVDTLKSTIPPSSACIASATNEVIFVSVGSELLNPVILSLSVYLMSGTETRRILVGCTGSV # ASIKIPLLVQELQCDKVDIKVVATEHALHFFDKDSLQVPVLTDRDEWENWKSVADPVLHIELRRWADILVIAPLDCNTLAKMANGICDNLLTCIVRAW # DLSKPLYFAPAMNTYMWQHPITAQQIETLKSYNYKEIPCIEKKLACGDTGFGAMAEVCTIVSSVKEALDLT] # sequence of block unknown_G 227 [GAMAEVCTIVSSVKEALDL] 246 # sequence of block unknown_F 211 [EIPCIEKKLACGDTG] 226 # sequence of block unknown_E 179 [KPLYFAPAMNTYMWQHPITAQQIETLK] 206 # sequence of block unknown_D 129 [SVADPVLHIELRRWADILVIAPLDCNTLAKMANGICDNLLTCIVRAWDL] 178 # sequence of block unknown_C 116 [PVLTDRDEWE] 126 # sequence of block unknown_B 93 [KVDIKVVATEHALHFFDKD] 112 # sequence of block unknown_A 69 [ILVGCTGSVASIKIPLLVQELQ] 91 # end gene g2 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370W44.prfl --predictionStart=0 --predictionEnd=37268 --species=fly ./tmp/Contig2907120180911_busco_2432604931_.temp