# 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..151]--> unknown_A (13) <--[4..7]--> unknown_B (11) <--[10..23]--> unknown_D (25) <--[10..37]--> unknown_F (45) <--[0..63]-- # BUSCO_20180911_busco_2432604931 version. Using default transition matrix. # admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0) # Looks like ./tmp/Contig3295520180911_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 = 10639, name = Contig32955) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig32955 AUGUSTUS gene 1 902 0.43 + . g1 Contig32955 AUGUSTUS transcript 1 902 0.43 + . g1.t1 Contig32955 AUGUSTUS intron 1 785 0.95 + . transcript_id "g1.t1"; gene_id "g1"; Contig32955 AUGUSTUS CDS 786 902 0.43 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig32955 AUGUSTUS stop_codon 900 902 . + 0 transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atagggaaagtggaggtgaaagacgtggattttaattctgatttcatcacaagaatgttaccaaaaatagactggacgg # ccttccaaaaagcagcaaaagaggtcggggattgttaa] # protein sequence = [IGKVEVKDVDFNSDFITRMLPKIDWTAFQKAAKEVGDC] # end gene g1 ### # start gene g2 Contig32955 AUGUSTUS gene 1543 7411 0.01 + . g2 Contig32955 AUGUSTUS transcript 1543 7411 0.01 + . g2.t1 Contig32955 AUGUSTUS start_codon 1543 1545 . + 0 transcript_id "g2.t1"; gene_id "g2"; Contig32955 AUGUSTUS intron 1559 2163 0.01 + . transcript_id "g2.t1"; gene_id "g2"; Contig32955 AUGUSTUS intron 2179 2507 0.01 + . transcript_id "g2.t1"; gene_id "g2"; Contig32955 AUGUSTUS intron 2539 3164 0.01 + . transcript_id "g2.t1"; gene_id "g2"; Contig32955 AUGUSTUS intron 3216 3323 0.01 + . transcript_id "g2.t1"; gene_id "g2"; Contig32955 AUGUSTUS intron 3336 3455 0.01 + . transcript_id "g2.t1"; gene_id "g2"; Contig32955 AUGUSTUS intron 3473 3790 0.01 + . transcript_id "g2.t1"; gene_id "g2"; Contig32955 AUGUSTUS intron 3803 5705 0.01 + . transcript_id "g2.t1"; gene_id "g2"; Contig32955 AUGUSTUS intron 5729 6035 0.01 + . transcript_id "g2.t1"; gene_id "g2"; Contig32955 AUGUSTUS intron 6129 7309 0.21 + . transcript_id "g2.t1"; gene_id "g2"; Contig32955 AUGUSTUS CDS 1543 1558 0.01 + 0 transcript_id "g2.t1"; gene_id "g2"; Contig32955 AUGUSTUS CDS 2164 2178 0.03 + 2 transcript_id "g2.t1"; gene_id "g2"; Contig32955 AUGUSTUS CDS 2508 2538 0.01 + 2 transcript_id "g2.t1"; gene_id "g2"; Contig32955 AUGUSTUS CDS 3165 3215 0.01 + 1 transcript_id "g2.t1"; gene_id "g2"; Contig32955 AUGUSTUS CDS 3324 3335 0.01 + 1 transcript_id "g2.t1"; gene_id "g2"; Contig32955 AUGUSTUS CDS 3456 3472 0.01 + 1 transcript_id "g2.t1"; gene_id "g2"; Contig32955 AUGUSTUS CDS 3791 3802 0.01 + 2 transcript_id "g2.t1"; gene_id "g2"; Contig32955 AUGUSTUS CDS 5706 5728 0.01 + 2 transcript_id "g2.t1"; gene_id "g2"; Contig32955 AUGUSTUS CDS 6036 6128 0.93 + 0 transcript_id "g2.t1"; gene_id "g2"; Contig32955 AUGUSTUS CDS 7310 7411 0.2 + 0 transcript_id "g2.t1"; gene_id "g2"; Contig32955 AUGUSTUS stop_codon 7409 7411 . + 0 transcript_id "g2.t1"; gene_id "g2"; Contig32955 AUGUSTUS protein_match 1543 1558 2.81 + 0 target "unknown_A[1..6]"; target_start 0; transcript_id "g2.t1"; gene_id "g2"; Contig32955 AUGUSTUS protein_match 2164 2178 1.45 + 1 target "unknown_A[6..11]"; target_start 0; transcript_id "g2.t1"; gene_id "g2"; Contig32955 AUGUSTUS protein_match 2508 2515 0.337 + 2 target "unknown_A[11..13]"; target_start 0; transcript_id "g2.t1"; gene_id "g2"; Contig32955 AUGUSTUS protein_match 2528 2538 0.979 + 0 target "unknown_B[1..4]"; target_start 17; transcript_id "g2.t1"; gene_id "g2"; Contig32955 AUGUSTUS protein_match 3165 3186 1.02 + 1 target "unknown_B[4..11]"; target_start 17; transcript_id "g2.t1"; gene_id "g2"; Contig32955 AUGUSTUS protein_match 3325 3335 1.04 + 0 target "unknown_D[1..4]"; target_start 38; transcript_id "g2.t1"; gene_id "g2"; Contig32955 AUGUSTUS protein_match 3456 3472 1.38 + 0 target "unknown_D[5..10]"; target_start 37; transcript_id "g2.t1"; gene_id "g2"; Contig32955 AUGUSTUS protein_match 3791 3802 1.99 + 1 target "unknown_D[10..14]"; target_start 37; transcript_id "g2.t1"; gene_id "g2"; Contig32955 AUGUSTUS protein_match 5706 5728 1.16 + 1 target "unknown_D[14..22]"; target_start 37; transcript_id "g2.t1"; gene_id "g2"; Contig32955 AUGUSTUS protein_match 6036 6047 1.4 + 0 target "unknown_D[22..25]"; target_start 38; transcript_id "g2.t1"; gene_id "g2"; Contig32955 AUGUSTUS protein_match 6090 6128 4.3 + 0 target "unknown_F[1..13]"; target_start 77; transcript_id "g2.t1"; gene_id "g2"; Contig32955 AUGUSTUS protein_match 7310 7405 7.5 + 0 target "unknown_F[14..45]"; target_start 77; transcript_id "g2.t1"; gene_id "g2"; # coding sequence = [atgaaaacaatttcgggccacattcttgccacctcaccggcaatggtgacatctcaatatgaacaaattaatgaggaca # cagacttcctgagaggtcacaatgctttgtttggtaattttggtatctctctgattggccgagagttatggacttttttgctagaatgtctggatatg # tgcggttatggagaaggattaccggagactatggaagacaaattaatggaggacacagacttcctgaagaaggtccacaatgctttgttggagatcga # ggtgatcgagggaaagctgatctgtccggagtctggccgggaatttcccatcagtaatggcatccctaatatgctactgaacgaagacgaagtgtga] # protein sequence = [MKTISGHILATSPAMVTSQYEQINEDTDFLRGHNALFGNFGISLIGRELWTFLLECLDMCGYGEGLPETMEDKLMEDT # DFLKKVHNALLEIEVIEGKLICPESGREFPISNGIPNMLLNEDEV] # sequence of block unknown_A 0 [MKTISGHILATSP] 13 # sequence of block unknown_B 17 [SQYEQINEDTD] 28 # sequence of block unknown_D 38 [NFGISLIGRELWTFLLECLDMCGYG] 63 # sequence of block unknown_F 77 [TDFLKKVHNALLEIEVIEGKLICPESGREFPISNGIPNMLLNEDE] 122 # end gene g2 ### # start gene g3 Contig32955 AUGUSTUS gene 7445 7666 0.21 + . g3 Contig32955 AUGUSTUS transcript 7445 7666 0.21 + . g3.t1 Contig32955 AUGUSTUS start_codon 7445 7447 . + 0 transcript_id "g3.t1"; gene_id "g3"; Contig32955 AUGUSTUS CDS 7445 7666 0.21 + 0 transcript_id "g3.t1"; gene_id "g3"; Contig32955 AUGUSTUS stop_codon 7664 7666 . + 0 transcript_id "g3.t1"; gene_id "g3"; # coding sequence = [atgtgtccagtagaatgtggaaggctggtggatgagtggttgttaaaatatgaaaggctgatggatgatagaatgtgga # tggacatgagagtggtttatagaatgagagtggatagaatgtggatggatgtgagagtggtggacagaatgtgggtggatgtgagagtggtggacaga # atgtggatggatgtgagagtggtggatggacgtgagagtgattga] # protein sequence = [MCPVECGRLVDEWLLKYERLMDDRMWMDMRVVYRMRVDRMWMDVRVVDRMWVDVRVVDRMWMDVRVVDGRESD] # end gene g3 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093711QY.prfl --predictionStart=0 --predictionEnd=27405 --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig3295520180911_busco_2432604931_.temp