# 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..270]--> unknown_A (19) <--[8..19]--> unknown_B (29) <--[2..21]--> unknown_C (48) <--[0..15]--> unknown_D (14) <--[0..34]--> unknown_E (23) <--[15..62]--> unknown_G (11) <--[7..19]--> unknown_I (19) <--[5..35]--> unknown_J (34) <--[1..38]--> unknown_K (12) <--[0..110]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig449620180911_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 = 19063, name = Contig4496) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig4496 AUGUSTUS gene 5066 15308 0.01 + . g1 Contig4496 AUGUSTUS transcript 5066 15308 0.01 + . g1.t1 Contig4496 AUGUSTUS tss 5066 5066 . + . transcript_id "g1.t1"; gene_id "g1"; Contig4496 AUGUSTUS exon 5066 5189 . + . transcript_id "g1.t1"; gene_id "g1"; Contig4496 AUGUSTUS exon 6994 7507 . + . transcript_id "g1.t1"; gene_id "g1"; Contig4496 AUGUSTUS start_codon 7019 7021 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig4496 AUGUSTUS intron 7508 7651 0.63 + . transcript_id "g1.t1"; gene_id "g1"; Contig4496 AUGUSTUS intron 7763 7953 0.07 + . transcript_id "g1.t1"; gene_id "g1"; Contig4496 AUGUSTUS intron 8083 8648 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig4496 AUGUSTUS intron 8991 13261 0.19 + . transcript_id "g1.t1"; gene_id "g1"; Contig4496 AUGUSTUS CDS 7019 7507 0.08 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig4496 AUGUSTUS CDS 7652 7762 0.54 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig4496 AUGUSTUS exon 7652 7762 . + . transcript_id "g1.t1"; gene_id "g1"; Contig4496 AUGUSTUS CDS 7954 8082 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig4496 AUGUSTUS exon 7954 8082 . + . transcript_id "g1.t1"; gene_id "g1"; Contig4496 AUGUSTUS CDS 8649 8990 0.34 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig4496 AUGUSTUS exon 8649 8990 . + . transcript_id "g1.t1"; gene_id "g1"; Contig4496 AUGUSTUS CDS 13262 13336 0.23 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig4496 AUGUSTUS exon 13262 15308 . + . transcript_id "g1.t1"; gene_id "g1"; Contig4496 AUGUSTUS stop_codon 13334 13336 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig4496 AUGUSTUS tts 15308 15308 . + . transcript_id "g1.t1"; gene_id "g1"; Contig4496 AUGUSTUS protein_match 7121 7177 4.13 + 0 target "unknown_A[1..19]"; target_start 34; transcript_id "g1.t1"; gene_id "g1"; Contig4496 AUGUSTUS protein_match 7208 7294 6.95 + 0 target "unknown_B[1..29]"; target_start 63; transcript_id "g1.t1"; gene_id "g1"; Contig4496 AUGUSTUS protein_match 7301 7444 4.03 + 0 target "unknown_C[1..48]"; target_start 94; transcript_id "g1.t1"; gene_id "g1"; Contig4496 AUGUSTUS protein_match 7448 7489 4.18 + 0 target "unknown_D[1..14]"; target_start 143; transcript_id "g1.t1"; gene_id "g1"; Contig4496 AUGUSTUS protein_match 7652 7720 4.49 + 0 target "unknown_E[1..23]"; target_start 163; transcript_id "g1.t1"; gene_id "g1"; Contig4496 AUGUSTUS protein_match 7963 7995 2.81 + 0 target "unknown_G[1..11]"; target_start 203; transcript_id "g1.t1"; gene_id "g1"; Contig4496 AUGUSTUS protein_match 8032 8082 1.19 + 0 target "unknown_I[1..17]"; target_start 226; transcript_id "g1.t1"; gene_id "g1"; Contig4496 AUGUSTUS protein_match 8649 8654 0.903 + 0 target "unknown_I[18..19]"; target_start 226; transcript_id "g1.t1"; gene_id "g1"; Contig4496 AUGUSTUS protein_match 8679 8780 3.22 + 0 target "unknown_J[1..34]"; target_start 253; transcript_id "g1.t1"; gene_id "g1"; Contig4496 AUGUSTUS protein_match 8814 8849 2.02 + 0 target "unknown_K[1..12]"; target_start 298; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgacgcagctcagttacaggagactgaagcagaaaatttatcttttatctgagtgttttctgttaaataagcgaagct # actctcaaaacaaaccaagacatcgagtgtttgtctccacttcagaggatatatacacaaatttagcgcttgaagaatggttgtatgaaagagaagat # ctgaaacagaaatccatacttttaatgtggcaaaataagcctgctgttgtgattggacgacatcagaatccgtggttagaatgcaatgttcccaaaat # aaaagaacatggcttcaagctcgctcgaagaattagtggaggggggtgtgtgtatcatgatcttggaaatctcaactgttcctttctgaaaacgagaa # ctttgtacaacaggaaggagaatctggacctggctgtgcgggccatcacttcccgctgggacgtggatttagaagtgaacgcccgagaagacattgtt # ctagacagactatacaaggtttcaggaacagcagctaagctgggaagaaacaacaccttccatcactttacactcctccatgatgtaaatgtggagaa # ccttgaaatgaccttggacagtcccatgaagatgggcgtccacagcaaagccactgatagtaagagatccaatataaagaatttgtcagagtgtgacg # tcactatagatttcacctcactggtggaggccataggtcaccaattttataaggcagctggaggggaaattgagtggatagacccgggagatgagact # ttgttccccggggtgatagaaatcagaaactcttcagaagattgggagtggatattcggtaaaactcctaaattttccataaacagaaaatttacctc # agaaaaacataaaactgaactgtctatgatgttcaactttgagaaaggcaggatccagggttctgagattacttgtgattgcgatgttccacatatca # cggagtttacagtcaggcttcagaatgacctaataggacggaggctgcacagagaggacttgaacccagttttacaggcttcagacttgtcaccactg # gattgtaaacaggttttccatgcccatgacatgagctgggctcactcactaaacctcacgtttatgaaggaaacactctaccactga] # protein sequence = [MTQLSYRRLKQKIYLLSECFLLNKRSYSQNKPRHRVFVSTSEDIYTNLALEEWLYEREDLKQKSILLMWQNKPAVVIG # RHQNPWLECNVPKIKEHGFKLARRISGGGCVYHDLGNLNCSFLKTRTLYNRKENLDLAVRAITSRWDVDLEVNAREDIVLDRLYKVSGTAAKLGRNNT # FHHFTLLHDVNVENLEMTLDSPMKMGVHSKATDSKRSNIKNLSECDVTIDFTSLVEAIGHQFYKAAGGEIEWIDPGDETLFPGVIEIRNSSEDWEWIF # GKTPKFSINRKFTSEKHKTELSMMFNFEKGRIQGSEITCDCDVPHITEFTVRLQNDLIGRRLHREDLNPVLQASDLSPLDCKQVFHAHDMSWAHSLNL # TFMKETLYH] # sequence of block unknown_A 34 [RVFVSTSEDIYTNLALEEW] 53 # sequence of block unknown_B 63 [SILLMWQNKPAVVIGRHQNPWLECNVPKI] 92 # sequence of block unknown_C 94 [HGFKLARRISGGGCVYHDLGNLNCSFLKTRTLYNRKENLDLAVRAITS] 142 # sequence of block unknown_D 143 [WDVDLEVNAREDIV] 157 # sequence of block unknown_E 163 [VSGTAAKLGRNNTFHHFTLLHDV] 186 # sequence of block unknown_G 203 [HSKATDSKRSN] 214 # sequence of block unknown_I 226 [FTSLVEAIGHQFYKAAGGE] 245 # sequence of block unknown_J 253 [ETLFPGVIEIRNSSEDWEWIFGKTPKFSINRKFT] 287 # sequence of block unknown_K 298 [FNFEKGRIQGSE] 310 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370HVI.prfl --predictionStart=0 --predictionEnd=27531 --species=fly ./tmp/Contig449620180911_busco_2432604931_.temp