# 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 # --[16..229]--> unknown_C (30) <--[12..180]--> unknown_D (26) <--[0..1]--> unknown_E (7) <--[9..13]--> unknown_G (18) <--[3..117]--> unknown_H (26) <--[5..135]--> unknown_I (25) <--[0..227]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig10742920180911_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 = 12578, name = Contig107429) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig107429 AUGUSTUS gene 3738 11095 0.01 - . g1 Contig107429 AUGUSTUS transcript 3738 11095 0.01 - . g1.t1 Contig107429 AUGUSTUS exon 3738 3957 . - . transcript_id "g1.t1"; gene_id "g1"; Contig107429 AUGUSTUS stop_codon 3921 3923 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig107429 AUGUSTUS intron 3958 4098 0.2 - . transcript_id "g1.t1"; gene_id "g1"; Contig107429 AUGUSTUS intron 4219 5498 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig107429 AUGUSTUS intron 5624 5930 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig107429 AUGUSTUS intron 6100 6441 0.94 - . transcript_id "g1.t1"; gene_id "g1"; Contig107429 AUGUSTUS intron 6580 9643 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig107429 AUGUSTUS intron 9688 10889 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig107429 AUGUSTUS CDS 3921 3957 0.21 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig107429 AUGUSTUS CDS 4099 4218 0.77 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig107429 AUGUSTUS exon 4099 4218 . - . transcript_id "g1.t1"; gene_id "g1"; Contig107429 AUGUSTUS CDS 5499 5623 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig107429 AUGUSTUS exon 5499 5623 . - . transcript_id "g1.t1"; gene_id "g1"; Contig107429 AUGUSTUS CDS 5931 6099 0.62 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig107429 AUGUSTUS exon 5931 6099 . - . transcript_id "g1.t1"; gene_id "g1"; Contig107429 AUGUSTUS CDS 6442 6579 0.01 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig107429 AUGUSTUS exon 6442 6579 . - . transcript_id "g1.t1"; gene_id "g1"; Contig107429 AUGUSTUS CDS 9644 9687 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig107429 AUGUSTUS exon 9644 9687 . - . transcript_id "g1.t1"; gene_id "g1"; Contig107429 AUGUSTUS CDS 10890 10925 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig107429 AUGUSTUS exon 10890 11095 . - . transcript_id "g1.t1"; gene_id "g1"; Contig107429 AUGUSTUS start_codon 10923 10925 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig107429 AUGUSTUS tss 11095 11095 . - . transcript_id "g1.t1"; gene_id "g1"; Contig107429 AUGUSTUS protein_match 4104 4178 8.28 - 0 target "unknown_I[1..25]"; target_start 184; transcript_id "g1.t1"; gene_id "g1"; Contig107429 AUGUSTUS protein_match 4200 4218 4.39 - 1 target "unknown_H[20..26]"; target_start 151; transcript_id "g1.t1"; gene_id "g1"; Contig107429 AUGUSTUS protein_match 5499 5557 5.13 - 0 target "unknown_H[1..20]"; target_start 151; transcript_id "g1.t1"; gene_id "g1"; Contig107429 AUGUSTUS protein_match 5579 5623 3.06 - 0 target "unknown_G[4..18]"; target_start 126; transcript_id "g1.t1"; gene_id "g1"; Contig107429 AUGUSTUS protein_match 5931 5939 2.41 - 0 target "unknown_G[1..3]"; target_start 126; transcript_id "g1.t1"; gene_id "g1"; Contig107429 AUGUSTUS protein_match 5970 5990 12.1 - 0 target "unknown_E[1..7]"; target_start 109; transcript_id "g1.t1"; gene_id "g1"; Contig107429 AUGUSTUS protein_match 5994 6071 4.29 - 0 target "unknown_D[1..26]"; target_start 82; transcript_id "g1.t1"; gene_id "g1"; Contig107429 AUGUSTUS protein_match 6516 6579 6.4 - 1 target "unknown_C[9..30]"; target_start 18; transcript_id "g1.t1"; gene_id "g1"; Contig107429 AUGUSTUS protein_match 9644 9669 1.05 - 0 target "unknown_C[1..9]"; target_start 18; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atggttcggaacgtttgtgacgtcacgttaattctcagagacagactgatttctaaattggacgttagaatccgcaatt # caatcgagagttactcgtgtaagatggccggtaatgataagaagctgtttaagctgatcagtcaggaaggaggggtggggccgctggatctccaggct # ctatctcctccccagaccgtgctgtcccacagtcccaccaaaaattacagtaagagttttggctcagtggagagcgagagttacctgtgtgatacgat # tcccacaaaaacgctcttctatctgatatcaacgctgaacgcttccttcaatccagattacgatttcagcaatgccaagagtgaagaattcagcaaag # agcccagcatcgattgggtggtgaacacagtagatacgcagctaaatgccacggcgggggaattattttctggattaaaacagactttgtgggcagca # attgacgaggaaatcactctccaggattgtgaagtctacagctacaatcctgatctgatctcggatccgtttggagaggaaggcagcatttggtcatt # taattactttctgtacaacaagaagctaaaacgaatcgttttcttcacgtgcagatcgtacagttggcagtttgactttgactttggttgggactgct # ag] # protein sequence = [MVRNVCDVTLILRDRLISKLDVRIRNSIESYSCKMAGNDKKLFKLISQEGGVGPLDLQALSPPQTVLSHSPTKNYSKS # FGSVESESYLCDTIPTKTLFYLISTLNASFNPDYDFSNAKSEEFSKEPSIDWVVNTVDTQLNATAGELFSGLKQTLWAAIDEEITLQDCEVYSYNPDL # ISDPFGEEGSIWSFNYFLYNKKLKRIVFFTCRSYSWQFDFDFGWDC] # sequence of block unknown_I 184 [GSIWSFNYFLYNKKLKRIVFFTCRS] 209 # sequence of block unknown_H 151 [QTLWAAIDEEITLQDCEVYSYNPDLI] 177 # sequence of block unknown_G 126 [SIDWVVNTVDTQLNATAG] 144 # sequence of block unknown_E 109 [PDYDFSN] 116 # sequence of block unknown_D 82 [ESESYLCDTIPTKTLFYLISTLNASF] 108 # sequence of block unknown_C 18 [KLDVRIRNSIESYSCKMAGNDKKLFKLISQ] 48 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG0937167R.prfl --predictionStart=0 --predictionEnd=24226 --species=fly ./tmp/Contig10742920180911_busco_2432604931_.temp