# 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 # --[36..395]--> unknown_D (12) <--[22..100]--> unknown_E (20) <--[1..24]--> unknown_F (13) <--[41..185]--> unknown_J (20) <--[0..109]--> unknown_K (44) <--[12..58]--> unknown_M (13) <--[0..49]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig3288420180911_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 = 19199, name = Contig32884) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig32884 AUGUSTUS gene 23 7885 0.01 - . g1 Contig32884 AUGUSTUS transcript 23 7885 0.01 - . g1.t1 Contig32884 AUGUSTUS tts 23 23 . - . transcript_id "g1.t1"; gene_id "g1"; Contig32884 AUGUSTUS exon 23 183 . - . transcript_id "g1.t1"; gene_id "g1"; Contig32884 AUGUSTUS exon 1152 1195 . - . transcript_id "g1.t1"; gene_id "g1"; Contig32884 AUGUSTUS exon 3877 5004 . - . transcript_id "g1.t1"; gene_id "g1"; Contig32884 AUGUSTUS stop_codon 4029 4031 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig32884 AUGUSTUS CDS 4029 4979 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig32884 AUGUSTUS start_codon 4977 4979 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig32884 AUGUSTUS exon 5596 5652 . - . transcript_id "g1.t1"; gene_id "g1"; Contig32884 AUGUSTUS exon 7816 7885 . - . transcript_id "g1.t1"; gene_id "g1"; Contig32884 AUGUSTUS tss 7885 7885 . - . transcript_id "g1.t1"; gene_id "g1"; Contig32884 AUGUSTUS protein_match 4038 4076 3.65 - 0 target "unknown_M[1..13]"; target_start 301; transcript_id "g1.t1"; gene_id "g1"; Contig32884 AUGUSTUS protein_match 4119 4250 4.88 - 0 target "unknown_K[1..44]"; target_start 243; transcript_id "g1.t1"; gene_id "g1"; Contig32884 AUGUSTUS protein_match 4368 4427 3.78 - 0 target "unknown_J[1..20]"; target_start 184; transcript_id "g1.t1"; gene_id "g1"; Contig32884 AUGUSTUS protein_match 4605 4643 4.22 - 0 target "unknown_F[1..13]"; target_start 112; transcript_id "g1.t1"; gene_id "g1"; Contig32884 AUGUSTUS protein_match 4647 4706 3.64 - 0 target "unknown_E[1..20]"; target_start 91; transcript_id "g1.t1"; gene_id "g1"; Contig32884 AUGUSTUS protein_match 4797 4832 4.05 - 0 target "unknown_D[1..12]"; target_start 49; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgtcaactcgaaatagtcaccctgtagccgttctacacaacgattatcagaaatctgtagaattaactgatgtttatg # tatcggtcattcaacataaaaaagaaactgtcgccatcgtcaaggctttatgtgaggattttccattagaaaacttcaaacatttgaaaagagtgagg # tcctccaaagaaggtcccctacaggtgatagtatgccatgacaaaaacaacttgaatgtaaaagaggttctgtcagatgttaaatatagttgcctcgg # aaaaccctttttaacgaaagtgccaaagctgaaaccattgacgagagcacagtttgaggaatcaaaactctattggccagtaacatttcatgaggata # aaaaagtgaccaaactcctaaacttgtcatacttttcacaagatgaattagatgcaatagatagacatgtccaagagttatttcaaattaaagaaagt # gagaaatcttgcagtgctgctttaatggtagacccaagaaataacaaagttttagcgagtacatgtgatagaagacatttgagtcatccattacagca # tgccgttatgctgtgtattgataaaatatctcactgtcaaggtggaggaatgtgggacatcgatgaacctgatgagagcgaagtagacagactaatga # caacgaaacagcagcaagaagatcaaggaagcatgacagataaatgtgatagaaaaatcaacaaacaagaattgtgcaatactcagtatctttgtaca # ggatatgacttatatgtaacaagagagccatgtgtaatgtgtgcaatggcattagtgcattccagaataggcagagtgttctatgtagaccctcatga # tgatgggggacttggttctcgatttcagattcacacggaaaaagaattgaaccataactttgaagttttcaaatgccaatcaccatga] # protein sequence = [MSTRNSHPVAVLHNDYQKSVELTDVYVSVIQHKKETVAIVKALCEDFPLENFKHLKRVRSSKEGPLQVIVCHDKNNLN # VKEVLSDVKYSCLGKPFLTKVPKLKPLTRAQFEESKLYWPVTFHEDKKVTKLLNLSYFSQDELDAIDRHVQELFQIKESEKSCSAALMVDPRNNKVLA # STCDRRHLSHPLQHAVMLCIDKISHCQGGGMWDIDEPDESEVDRLMTTKQQQEDQGSMTDKCDRKINKQELCNTQYLCTGYDLYVTREPCVMCAMALV # HSRIGRVFYVDPHDDGGLGSRFQIHTEKELNHNFEVFKCQSP] # sequence of block unknown_M 301 [KELNHNFEVFKCQ] 314 # sequence of block unknown_K 243 [KQELCNTQYLCTGYDLYVTREPCVMCAMALVHSRIGRVFYVDPH] 287 # sequence of block unknown_J 184 [SHPLQHAVMLCIDKISHCQG] 204 # sequence of block unknown_F 112 [SKLYWPVTFHEDK] 125 # sequence of block unknown_E 91 [GKPFLTKVPKLKPLTRAQFE] 111 # sequence of block unknown_D 49 [ENFKHLKRVRSS] 61 # end gene g1 ### # start gene g2 Contig32884 AUGUSTUS gene 8216 14346 0.01 + . g2 Contig32884 AUGUSTUS transcript 8216 14346 0.01 + . g2.t1 Contig32884 AUGUSTUS tss 8216 8216 . + . transcript_id "g2.t1"; gene_id "g2"; Contig32884 AUGUSTUS exon 8216 8359 . + . transcript_id "g2.t1"; gene_id "g2"; Contig32884 AUGUSTUS start_codon 8278 8280 . + 0 transcript_id "g2.t1"; gene_id "g2"; Contig32884 AUGUSTUS intron 8360 8545 1 + . transcript_id "g2.t1"; gene_id "g2"; Contig32884 AUGUSTUS intron 8753 9652 0.58 + . transcript_id "g2.t1"; gene_id "g2"; Contig32884 AUGUSTUS intron 9718 9965 0.99 + . transcript_id "g2.t1"; gene_id "g2"; Contig32884 AUGUSTUS intron 10186 10709 0.77 + . transcript_id "g2.t1"; gene_id "g2"; Contig32884 AUGUSTUS intron 10837 12446 0.07 + . transcript_id "g2.t1"; gene_id "g2"; Contig32884 AUGUSTUS CDS 8278 8359 0.1 + 0 transcript_id "g2.t1"; gene_id "g2"; Contig32884 AUGUSTUS CDS 8546 8752 1 + 2 transcript_id "g2.t1"; gene_id "g2"; Contig32884 AUGUSTUS exon 8546 8752 . + . transcript_id "g2.t1"; gene_id "g2"; Contig32884 AUGUSTUS CDS 9653 9717 0.62 + 2 transcript_id "g2.t1"; gene_id "g2"; Contig32884 AUGUSTUS exon 9653 9717 . + . transcript_id "g2.t1"; gene_id "g2"; Contig32884 AUGUSTUS CDS 9966 10185 1 + 0 transcript_id "g2.t1"; gene_id "g2"; Contig32884 AUGUSTUS exon 9966 10185 . + . transcript_id "g2.t1"; gene_id "g2"; Contig32884 AUGUSTUS CDS 10710 10836 0.25 + 2 transcript_id "g2.t1"; gene_id "g2"; Contig32884 AUGUSTUS exon 10710 10836 . + . transcript_id "g2.t1"; gene_id "g2"; Contig32884 AUGUSTUS CDS 12447 12630 0.14 + 1 transcript_id "g2.t1"; gene_id "g2"; Contig32884 AUGUSTUS exon 12447 14346 . + . transcript_id "g2.t1"; gene_id "g2"; Contig32884 AUGUSTUS stop_codon 12628 12630 . + 0 transcript_id "g2.t1"; gene_id "g2"; Contig32884 AUGUSTUS tts 14346 14346 . + . transcript_id "g2.t1"; gene_id "g2"; # coding sequence = [atgtatttcacctcatctgctccgtttgaattctctgcattctatggaaacaacgatgatccatttgctcaattcttca # ccagttctggtaactcgggtgaatattccaaaaagaaagagaaagagaggaaacgaaatgttgcagaagagtatggatttaatgaagatattaatgag # gaatacctgttttctcctcgacaaggaaagtctcggatgtacgatggtttgtctgacacggatgatgagccaacgttcaggtttagcatgtcggagtc # cgaatcggatccagatgattatgaggaaaccaggtttaagtgctctttctgtgggaagatgttgaagattgacactttgaaaactcatgaacctgctt # gcggacgactgcgcaagaaagaagtgaacattgacagtgatgatgagtactttgatgctaacggttactcgtcgaagtttggtccatccaaagtacct # ggggattggagaggcacccacgaagaactccttagacacatccgacgacagcgcagagcttccaagtccaagaaacgtgaagaggaacttaaaagtga # tctggtattcaaagaaaattcccaaacccaggagacaaaaaacacctcacgaagaaaaggagaacgagtcgccccctaccaccaccaggagtcgcccc # acaagctaccccgacctgaacgacaccaggcccaagctagacagggaaccaccacgggagcctactttggggtatctggttctcgattcggtgccacc # agtacaaagtacggaggaggacttaaaggatcctcagttcatggaacggggttcaaagggtcaaatacaagagggacaggaacctatcacaaaccaac # cactgttaagttcgctacttag] # protein sequence = [MYFTSSAPFEFSAFYGNNDDPFAQFFTSSGNSGEYSKKKEKERKRNVAEEYGFNEDINEEYLFSPRQGKSRMYDGLSD # TDDEPTFRFSMSESESDPDDYEETRFKCSFCGKMLKIDTLKTHEPACGRLRKKEVNIDSDDEYFDANGYSSKFGPSKVPGDWRGTHEELLRHIRRQRR # ASKSKKREEELKSDLVFKENSQTQETKNTSRRKGERVAPYHHQESPHKLPRPERHQAQARQGTTTGAYFGVSGSRFGATSTKYGGGLKGSSVHGTGFK # GSNTRGTGTYHKPTTVKFAT] # end gene g2 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093716T7.prfl --predictionStart=0 --predictionEnd=24823 --species=fly ./tmp/Contig3288420180911_busco_2432604931_.temp