# 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 # --[10..38]--> unknown_A (22) <--[10..28]--> unknown_C (36) <--[0..2]--> unknown_D (17) <--[18..26]--> unknown_F (14) <--[7..33]--> unknown_G (8) <--[1..21]--> unknown_H (31) <--[0..9]--> unknown_I (12) <--[2..4]--> unknown_J (51) <--[0..21]--> unknown_K (10) <--[0..2]--> unknown_L (23) <--[0..45]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig309120180911_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 = 18397, name = Contig3091) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig3091 AUGUSTUS gene 7133 11435 0.01 - . g1 Contig3091 AUGUSTUS transcript 7133 11435 0.01 - . g1.t1 Contig3091 AUGUSTUS tts 7133 7133 . - . transcript_id "g1.t1"; gene_id "g1"; Contig3091 AUGUSTUS exon 7133 7560 . - . transcript_id "g1.t1"; gene_id "g1"; Contig3091 AUGUSTUS stop_codon 7241 7243 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig3091 AUGUSTUS intron 7561 8615 0.72 - . transcript_id "g1.t1"; gene_id "g1"; Contig3091 AUGUSTUS intron 8863 9836 0.35 - . transcript_id "g1.t1"; gene_id "g1"; Contig3091 AUGUSTUS intron 9914 11057 0.45 - . transcript_id "g1.t1"; gene_id "g1"; Contig3091 AUGUSTUS CDS 7241 7560 0.7 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig3091 AUGUSTUS CDS 8616 8862 0.26 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig3091 AUGUSTUS exon 8616 8862 . - . transcript_id "g1.t1"; gene_id "g1"; Contig3091 AUGUSTUS CDS 9837 9913 0.47 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig3091 AUGUSTUS exon 9837 9913 . - . transcript_id "g1.t1"; gene_id "g1"; Contig3091 AUGUSTUS CDS 11058 11340 0.12 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig3091 AUGUSTUS exon 11058 11435 . - . transcript_id "g1.t1"; gene_id "g1"; Contig3091 AUGUSTUS start_codon 11338 11340 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig3091 AUGUSTUS tss 11435 11435 . - . transcript_id "g1.t1"; gene_id "g1"; Contig3091 AUGUSTUS protein_match 7295 7363 5.98 - 0 target "unknown_L[1..23]"; target_start 268; transcript_id "g1.t1"; gene_id "g1"; Contig3091 AUGUSTUS protein_match 7364 7393 3.63 - 0 target "unknown_K[1..10]"; target_start 258; transcript_id "g1.t1"; gene_id "g1"; Contig3091 AUGUSTUS protein_match 7394 7546 6.74 - 0 target "unknown_J[1..51]"; target_start 207; transcript_id "g1.t1"; gene_id "g1"; Contig3091 AUGUSTUS protein_match 7553 7560 5.21 - 2 target "unknown_I[10..12]"; target_start 193; transcript_id "g1.t1"; gene_id "g1"; Contig3091 AUGUSTUS protein_match 8616 8643 3.69 - 0 target "unknown_I[1..10]"; target_start 193; transcript_id "g1.t1"; gene_id "g1"; Contig3091 AUGUSTUS protein_match 8644 8736 5.39 - 0 target "unknown_H[1..31]"; target_start 162; transcript_id "g1.t1"; gene_id "g1"; Contig3091 AUGUSTUS protein_match 8743 8766 5.1 - 0 target "unknown_G[1..8]"; target_start 152; transcript_id "g1.t1"; gene_id "g1"; Contig3091 AUGUSTUS protein_match 8812 8853 5.48 - 0 target "unknown_F[1..14]"; target_start 123; transcript_id "g1.t1"; gene_id "g1"; Contig3091 AUGUSTUS protein_match 9885 9913 5.69 - 2 target "unknown_D[8..17]"; target_start 87; transcript_id "g1.t1"; gene_id "g1"; Contig3091 AUGUSTUS protein_match 11058 11079 13.8 - 0 target "unknown_D[1..8]"; target_start 87; transcript_id "g1.t1"; gene_id "g1"; Contig3091 AUGUSTUS protein_match 11080 11187 5.06 - 0 target "unknown_C[1..36]"; target_start 51; transcript_id "g1.t1"; gene_id "g1"; Contig3091 AUGUSTUS protein_match 11221 11286 4.79 - 0 target "unknown_A[1..22]"; target_start 18; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgtccacttcagcagatgaaacctctgtccaagtagttggtaacattttgacagacgtagcgaaacctctgaaggaca # gattccgagcgttgtttaccttgcgtaacattgggggagaaaaggccattgacattatatccagctgctttaatgacacgtctgctcttcttaaacat # gaattggcatactgtcttggccaaatgcaggacaaatatgctctgaatgccttgtcccatgttttggcagatcgttcacaggagcccatggttcgaca # tgaagcaggtgaagcattgggagccattggagcacaggagtctgtcagtgtcttgaaagaatatcttaatgatccagtaatagaggttgcggaaacct # gtcagttatctctccagagactgaactggctcaacagcagcaaggagagtgagaataacttactaccaaatccttataagtctgtagaccctgctcca # tcaacagggaaaatggaggttatggaattggagaagattttgttggatgaatttctaccccttttccagagatacagggccatgttttctctcagaaa # tctaggaacaaaggaagctgtgaaagtgttggctaaagggctcaaatgtaccagtgccctgtttcgccatgaaattgcttatgtccttggtcaaattc # agagtgatgcctgtgtagatgaactaaaaactaacctccaggatatggaggagaacccaatggtgagacacgagtgtgcagaagccctcggatccatt # gctaccccagaatgcaccagtattttagaggaatacctaaaagacaatgaacgagtggttaaagagagctgtcttgtggcactagatatcagtgaata # tgagaacagtgcacagttccaatatgctgatggtttggctaagttaaatacagttcaaagttaa] # protein sequence = [MSTSADETSVQVVGNILTDVAKPLKDRFRALFTLRNIGGEKAIDIISSCFNDTSALLKHELAYCLGQMQDKYALNALS # HVLADRSQEPMVRHEAGEALGAIGAQESVSVLKEYLNDPVIEVAETCQLSLQRLNWLNSSKESENNLLPNPYKSVDPAPSTGKMEVMELEKILLDEFL # PLFQRYRAMFSLRNLGTKEAVKVLAKGLKCTSALFRHEIAYVLGQIQSDACVDELKTNLQDMEENPMVRHECAEALGSIATPECTSILEEYLKDNERV # VKESCLVALDISEYENSAQFQYADGLAKLNTVQS] # sequence of block unknown_L 268 [KDNERVVKESCLVALDISEYENS] 291 # sequence of block unknown_K 258 [ECTSILEEYL] 268 # sequence of block unknown_J 207 [SALFRHEIAYVLGQIQSDACVDELKTNLQDMEENPMVRHECAEALGSIATP] 258 # sequence of block unknown_I 193 [KEAVKVLAKGLK] 205 # sequence of block unknown_H 162 [EVMELEKILLDEFLPLFQRYRAMFSLRNLGT] 193 # sequence of block unknown_G 152 [VDPAPSTG] 160 # sequence of block unknown_F 123 [TCQLSLQRLNWLNS] 137 # sequence of block unknown_D 87 [PMVRHEAGEALGAIGAQ] 104 # sequence of block unknown_C 51 [DTSALLKHELAYCLGQMQDKYALNALSHVLADRSQE] 87 # sequence of block unknown_A 18 [DVAKPLKDRFRALFTLRNIGGE] 40 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370TP2.prfl --predictionStart=0 --predictionEnd=31262 --species=fly ./tmp/Contig309120180911_busco_2432604931_.temp