# 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..97]--> unknown_A (30) <--[1..3]--> unknown_B (38) <--[0..22]--> unknown_C (25) <--[0..19]--> unknown_D (12) <--[14..110]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig2600720180911_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 = 35209, name = Contig26007) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig26007 AUGUSTUS gene 48114 49897 0.09 + . g1 Contig26007 AUGUSTUS transcript 48114 49897 0.09 + . g1.t1 Contig26007 AUGUSTUS tss 48114 48114 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26007 AUGUSTUS exon 48114 49897 . + . transcript_id "g1.t1"; gene_id "g1"; Contig26007 AUGUSTUS start_codon 48193 48195 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig26007 AUGUSTUS CDS 48193 49848 0.72 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig26007 AUGUSTUS stop_codon 49846 49848 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig26007 AUGUSTUS tts 49897 49897 . + . transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atggcaacaggatatgaagatcatgcttcgaagcgcatgaagatggacaaatccagtgaggatcccatcaagccttccc # cgtcccccgttgtccatgtgagaggtctctatgacaacatcatggagcgggacctgacacgggccgtccagcagtttgggacggtcagctacgtcgtg # cttatgccaaagaaacaccaggctttgatcgagtttgaagatatctccggagccacaaattgtgttaattactcaaatgagaaccaaatatttgtggc # cggtcagccagcctatttcaactactccaccagtcagcacattcaaagacccggtccaaaagacgacaacaggcccacaaatcacatcctgctgttca # ccatcttgaatcctcagtacccggtcaccgtcgacatcatgcacacaatctgtagcccttacggacaagtggtgcggatcgtcatctttaggaacagc # ggcatgcagagtatggtcgagtttgataacgtagaatctgccaaacgagccaagcaagctttaaacggtgctgacatttactcggactgtaatacact # gaaaatagagtatgcaaaaacagacaaactcaatgtgtttaaaaatgaccagaacagctgggactactccaatccaaacttgaacagcgaagctgcac # ctcccagaaatatgccacttctgccagagccaggcggtggcaacactccattcaacaggagaccaggtccaggggcacaggcaggatttggaggatac # ggaagagaagcaggcccaaatcagagttaccaaggttaccagggagggggctatggtgggggaatgtatgaccaaggcgatgggttcagtcagggcta # tggagctatgcctcagaggcagggaggcttcgggcaggagggatttggaagaaaacctggaccgccacaaatgcacgatgaaggaggttatggccgtc # cgatgccgccgcacggttatcaagaccaaggtggaccacatccggggtccatgattcagggggcagttgtcatggcatatggtttgaatccggatcac # attaactgtgacagactatttaacattttctgtttgtatggaaatgttgctagagtcaagtttctaaaaagtaaagaaggatcagccatgatacagat # gggagactcgttggctgtggaaagaagcatccagaatctcagtcacgtcactttgtttggaagcaagttaacgctagctgtctccaaacaggcattct # tacaagatgttccaaatccttatgaattaccagatggatcgccatccttcaaagacttcatgggaagcaggaacaacagatacgcaaatcctgagcag # gccagcaaaaacagaatcatggctcctacaaaggttctacactacttcaatgttcctccagatatgtcggaaaaagttttagaggaagttttcaccaa # cgtaggagcagaatgtccgcagaaagttaaacagtttcccgccaccagcgcaagaagttcatcaggactggttcaatttaaagacatcgaggaagctg # taaacgccctggccttggctaaccacgcttcaattcccaatccttctggaaaaagcccatacgtgatgaaactctgcttttctggcagtcctattggt # ggacgatag] # protein sequence = [MATGYEDHASKRMKMDKSSEDPIKPSPSPVVHVRGLYDNIMERDLTRAVQQFGTVSYVVLMPKKHQALIEFEDISGAT # NCVNYSNENQIFVAGQPAYFNYSTSQHIQRPGPKDDNRPTNHILLFTILNPQYPVTVDIMHTICSPYGQVVRIVIFRNSGMQSMVEFDNVESAKRAKQ # ALNGADIYSDCNTLKIEYAKTDKLNVFKNDQNSWDYSNPNLNSEAAPPRNMPLLPEPGGGNTPFNRRPGPGAQAGFGGYGREAGPNQSYQGYQGGGYG # GGMYDQGDGFSQGYGAMPQRQGGFGQEGFGRKPGPPQMHDEGGYGRPMPPHGYQDQGGPHPGSMIQGAVVMAYGLNPDHINCDRLFNIFCLYGNVARV # KFLKSKEGSAMIQMGDSLAVERSIQNLSHVTLFGSKLTLAVSKQAFLQDVPNPYELPDGSPSFKDFMGSRNNRYANPEQASKNRIMAPTKVLHYFNVP # PDMSEKVLEEVFTNVGAECPQKVKQFPATSARSSSGLVQFKDIEEAVNALALANHASIPNPSGKSPYVMKLCFSGSPIGGR] # end gene g1 ### # start gene g2 Contig26007 AUGUSTUS gene 53318 63483 0.01 - . g2 Contig26007 AUGUSTUS transcript 53318 63483 0.01 - . g2.t1 Contig26007 AUGUSTUS tts 53318 53318 . - . transcript_id "g2.t1"; gene_id "g2"; Contig26007 AUGUSTUS exon 53318 53850 . - . transcript_id "g2.t1"; gene_id "g2"; Contig26007 AUGUSTUS stop_codon 53732 53734 . - 0 transcript_id "g2.t1"; gene_id "g2"; Contig26007 AUGUSTUS intron 53851 54254 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig26007 AUGUSTUS intron 54385 56249 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig26007 AUGUSTUS intron 56310 57485 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig26007 AUGUSTUS intron 57635 57930 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig26007 AUGUSTUS intron 58000 60860 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig26007 AUGUSTUS CDS 53732 53850 0.04 - 2 transcript_id "g2.t1"; gene_id "g2"; Contig26007 AUGUSTUS CDS 54255 54384 0.01 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig26007 AUGUSTUS exon 54255 54384 . - . transcript_id "g2.t1"; gene_id "g2"; Contig26007 AUGUSTUS CDS 56250 56309 0.01 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig26007 AUGUSTUS exon 56250 56309 . - . transcript_id "g2.t1"; gene_id "g2"; Contig26007 AUGUSTUS CDS 57486 57634 0.01 - 2 transcript_id "g2.t1"; gene_id "g2"; Contig26007 AUGUSTUS exon 57486 57634 . - . transcript_id "g2.t1"; gene_id "g2"; Contig26007 AUGUSTUS CDS 57931 57999 0.01 - 2 transcript_id "g2.t1"; gene_id "g2"; Contig26007 AUGUSTUS exon 57931 57999 . - . transcript_id "g2.t1"; gene_id "g2"; Contig26007 AUGUSTUS CDS 60861 60942 0.25 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig26007 AUGUSTUS exon 60861 60950 . - . transcript_id "g2.t1"; gene_id "g2"; Contig26007 AUGUSTUS start_codon 60940 60942 . - 0 transcript_id "g2.t1"; gene_id "g2"; Contig26007 AUGUSTUS exon 63348 63483 . - . transcript_id "g2.t1"; gene_id "g2"; Contig26007 AUGUSTUS tss 63483 63483 . - . transcript_id "g2.t1"; gene_id "g2"; Contig26007 AUGUSTUS protein_match 54310 54345 3.73 - 0 target "unknown_D[1..12]"; target_start 133; transcript_id "g2.t1"; gene_id "g2"; Contig26007 AUGUSTUS protein_match 54346 54384 6.8 - 0 target "unknown_C[13..25]"; target_start 108; transcript_id "g2.t1"; gene_id "g2"; Contig26007 AUGUSTUS protein_match 56250 56285 3.49 - 0 target "unknown_C[1..12]"; target_start 108; transcript_id "g2.t1"; gene_id "g2"; Contig26007 AUGUSTUS protein_match 56286 56309 7.57 - 0 target "unknown_B[31..38]"; target_start 70; transcript_id "g2.t1"; gene_id "g2"; Contig26007 AUGUSTUS protein_match 57486 57575 8.2 - 0 target "unknown_B[1..30]"; target_start 70; transcript_id "g2.t1"; gene_id "g2"; Contig26007 AUGUSTUS protein_match 57579 57634 5.44 - 2 target "unknown_A[12..30]"; target_start 39; transcript_id "g2.t1"; gene_id "g2"; Contig26007 AUGUSTUS protein_match 57931 57964 5.37 - 0 target "unknown_A[1..12]"; target_start 39; transcript_id "g2.t1"; gene_id "g2"; # coding sequence = [atgtctagaggaggatttaggagcaactacggtggcggcggcagaggtggaggaagagggggtggattccgcgggggtg # gagggggccgaggtggaggacgagggggatatggtaacagatacgatcaaggccccccagaaactgttaaagaactcggggagtacgttcatccttgt # gaagatgaccttgtctgcgtcagcacgatagaggacgtcccacattttaatgctccaatttttctagaaaacaaacaacagattggaaaagtggacga # gatctttggatccattagaaatttttatttttcagtaaaattatcagaaaacatgaaagcaaaatcatttgccaaaagcacaaagttatttatagatc # cctacaaattgttaccactccagagatttctgcccgggtctggaggagggagaggtagaggacgaggcggggggcggggccgtggaggaggcagaggg # ggagggggcagaggacgagacgtcaacctggtattctggtaccccctgaagaaaattggttatcaagacacatggttaaagaaacaactagttatttg # gaaatgcctgctcagtatcttcatggtggttaaattttga] # protein sequence = [MSRGGFRSNYGGGGRGGGRGGGFRGGGGGRGGGRGGYGNRYDQGPPETVKELGEYVHPCEDDLVCVSTIEDVPHFNAP # IFLENKQQIGKVDEIFGSIRNFYFSVKLSENMKAKSFAKSTKLFIDPYKLLPLQRFLPGSGGGRGRGRGGGRGRGGGRGGGGRGRDVNLVFWYPLKKI # GYQDTWLKKQLVIWKCLLSIFMVVKF] # sequence of block unknown_D 133 [FLPGSGGGRGRG] 145 # sequence of block unknown_C 108 [NMKAKSFAKSTKLFIDPYKLLPLQR] 133 # sequence of block unknown_B 70 [DVPHFNAPIFLENKQQIGKVDEIFGSIRNFYFSVKLSE] 108 # sequence of block unknown_A 39 [RYDQGPPETVKELGEYVHPCEDDLVCVSTI] 69 # end gene g2 ### # start gene g3 Contig26007 AUGUSTUS gene 63654 72697 0.02 + . g3 Contig26007 AUGUSTUS transcript 63654 72697 0.02 + . g3.t1 Contig26007 AUGUSTUS tss 63654 63654 . + . transcript_id "g3.t1"; gene_id "g3"; Contig26007 AUGUSTUS exon 63654 63992 . + . transcript_id "g3.t1"; gene_id "g3"; Contig26007 AUGUSTUS exon 64740 65097 . + . transcript_id "g3.t1"; gene_id "g3"; Contig26007 AUGUSTUS start_codon 65016 65018 . + 0 transcript_id "g3.t1"; gene_id "g3"; Contig26007 AUGUSTUS intron 65098 67537 0.78 + . transcript_id "g3.t1"; gene_id "g3"; Contig26007 AUGUSTUS intron 67827 69719 0.39 + . transcript_id "g3.t1"; gene_id "g3"; Contig26007 AUGUSTUS intron 69832 72697 0.04 + . transcript_id "g3.t1"; gene_id "g3"; Contig26007 AUGUSTUS CDS 65016 65097 0.6 + 0 transcript_id "g3.t1"; gene_id "g3"; Contig26007 AUGUSTUS CDS 67538 67826 0.59 + 2 transcript_id "g3.t1"; gene_id "g3"; Contig26007 AUGUSTUS exon 67538 67826 . + . transcript_id "g3.t1"; gene_id "g3"; Contig26007 AUGUSTUS CDS 69720 69831 0.32 + 1 transcript_id "g3.t1"; gene_id "g3"; Contig26007 AUGUSTUS exon 69720 69831 . + . transcript_id "g3.t1"; gene_id "g3"; # coding sequence = [atggatgctgtccagaactatttctacaacgttactggtgaaccaaagcatataccggtctccatttgtggaaaagggg # gaggtcatacagacgaagatcacggtccagaagtgattcacgtgatcgggacaggaagaggcgaagtcgatctagaagtcgacccagaaggtctcgat # cccgagatagatcacgaagatccagatccagagagaggaagcgatctcattcccgtgagaggagaaggtctagagatagagatagaagaaggtcacga # tctagagacaggagaaggtcaaagagatcaaggtcaaggaacagaaagtaagagaattcagtatattcctgaatgttactgtgatttgcagcaatgaa # agtcgagatccaaaactccagacaagaaaaaaagaagtatatcaccggaggcaaagaaattgacgcattgtgagggggagatcactgtcaaggatgag # cccctggacaag] # protein sequence = [MDAVQNYFYNVTGEPKHIPVSICGKGGGHTDEDHGPEVIHVIGTGRGEVDLEVDPEGLDPEIDHEDPDPERGSDLIPV # RGEGLEIEIEEGHDLETGEGQRDQGQGTESKRIQYIPECYCDLQQXKSRSKTPDKKKRSISPEAKKLTHCEGEITVKDEPLDK] # end gene g3 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093713LY.prfl --predictionStart=37489 --predictionEnd=77641 --species=fly ./tmp/Contig2600720180911_busco_2432604931_.temp