# 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..190]--> unknown_A (11) <--[0..9]--> unknown_B (10) <--[5..27]--> unknown_C (13) <--[4..7]--> unknown_D (33) <--[6..15]--> unknown_E (28) <--[2..9]--> unknown_F (10) <--[3..6]--> unknown_G (19) <--[0..3]--> unknown_H (31) <--[0..30]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig3034520180911_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 = 35784, name = Contig30345) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig30345 AUGUSTUS gene 689 10695 0.02 - . g1 Contig30345 AUGUSTUS transcript 689 10695 0.02 - . g1.t1 Contig30345 AUGUSTUS exon 689 1079 . - . transcript_id "g1.t1"; gene_id "g1"; Contig30345 AUGUSTUS stop_codon 966 968 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig30345 AUGUSTUS intron 1080 6821 0.36 - . transcript_id "g1.t1"; gene_id "g1"; Contig30345 AUGUSTUS intron 6962 10581 0.28 - . transcript_id "g1.t1"; gene_id "g1"; Contig30345 AUGUSTUS CDS 966 1079 0.37 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig30345 AUGUSTUS CDS 6822 6961 0.68 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig30345 AUGUSTUS exon 6822 6961 . - . transcript_id "g1.t1"; gene_id "g1"; Contig30345 AUGUSTUS CDS 10582 10624 0.49 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig30345 AUGUSTUS exon 10582 10695 . - . transcript_id "g1.t1"; gene_id "g1"; Contig30345 AUGUSTUS start_codon 10622 10624 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig30345 AUGUSTUS tss 10695 10695 . - . transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgtcgcggcatcgtaatgtacggactatgaactatgaggatgctcggctgaattcctgcctggaggagattggaaacg # tcctgggagacaccattccggagcacattgtttcacagactgtggtgaagaaccagtacaacatccaggcatctctgaacgagctcctcaataaaaat # ggtacgcgagccactgattcgtacaaccgtctacagaagaaaccgacacaaacgggactcgtaaaatccgccattaactcgaataagacactgcacca # agtgcccggtaaaacgctgtga] # protein sequence = [MSRHRNVRTMNYEDARLNSCLEEIGNVLGDTIPEHIVSQTVVKNQYNIQASLNELLNKNGTRATDSYNRLQKKPTQTG # LVKSAINSNKTLHQVPGKTL] # end gene g1 ### # start gene g2 Contig30345 AUGUSTUS gene 11916 17003 0.01 + . g2 Contig30345 AUGUSTUS transcript 11916 17003 0.01 + . g2.t1 Contig30345 AUGUSTUS tss 11916 11916 . + . transcript_id "g2.t1"; gene_id "g2"; Contig30345 AUGUSTUS exon 11916 12095 . + . transcript_id "g2.t1"; gene_id "g2"; Contig30345 AUGUSTUS start_codon 12060 12062 . + 0 transcript_id "g2.t1"; gene_id "g2"; Contig30345 AUGUSTUS intron 12096 13206 0.05 + . transcript_id "g2.t1"; gene_id "g2"; Contig30345 AUGUSTUS intron 13324 14424 0.1 + . transcript_id "g2.t1"; gene_id "g2"; Contig30345 AUGUSTUS intron 14618 15518 0.02 + . transcript_id "g2.t1"; gene_id "g2"; Contig30345 AUGUSTUS CDS 12060 12095 0.38 + 0 transcript_id "g2.t1"; gene_id "g2"; Contig30345 AUGUSTUS CDS 13207 13323 0.07 + 0 transcript_id "g2.t1"; gene_id "g2"; Contig30345 AUGUSTUS exon 13207 13323 . + . transcript_id "g2.t1"; gene_id "g2"; Contig30345 AUGUSTUS CDS 14425 14617 0.29 + 0 transcript_id "g2.t1"; gene_id "g2"; Contig30345 AUGUSTUS exon 14425 14617 . + . transcript_id "g2.t1"; gene_id "g2"; Contig30345 AUGUSTUS CDS 15519 15802 0.02 + 2 transcript_id "g2.t1"; gene_id "g2"; Contig30345 AUGUSTUS exon 15519 17003 . + . transcript_id "g2.t1"; gene_id "g2"; Contig30345 AUGUSTUS stop_codon 15800 15802 . + 0 transcript_id "g2.t1"; gene_id "g2"; Contig30345 AUGUSTUS tts 17003 17003 . + . transcript_id "g2.t1"; gene_id "g2"; Contig30345 AUGUSTUS protein_match 13240 13272 2.97 + 0 target "unknown_A[1..11]"; target_start 23; transcript_id "g2.t1"; gene_id "g2"; Contig30345 AUGUSTUS protein_match 13273 13302 4.23 + 0 target "unknown_B[1..10]"; target_start 34; transcript_id "g2.t1"; gene_id "g2"; Contig30345 AUGUSTUS protein_match 14431 14469 5.85 + 0 target "unknown_C[1..13]"; target_start 53; transcript_id "g2.t1"; gene_id "g2"; Contig30345 AUGUSTUS protein_match 14482 14580 5.7 + 0 target "unknown_D[1..33]"; target_start 70; transcript_id "g2.t1"; gene_id "g2"; Contig30345 AUGUSTUS protein_match 14605 14617 4.6 + 0 target "unknown_E[1..5]"; target_start 111; transcript_id "g2.t1"; gene_id "g2"; Contig30345 AUGUSTUS protein_match 15519 15589 5.74 + 2 target "unknown_E[5..28]"; target_start 111; transcript_id "g2.t1"; gene_id "g2"; Contig30345 AUGUSTUS protein_match 15602 15631 3.86 + 0 target "unknown_F[1..10]"; target_start 143; transcript_id "g2.t1"; gene_id "g2"; Contig30345 AUGUSTUS protein_match 15641 15697 8.99 + 0 target "unknown_G[1..19]"; target_start 156; transcript_id "g2.t1"; gene_id "g2"; Contig30345 AUGUSTUS protein_match 15704 15796 3.94 + 0 target "unknown_H[1..31]"; target_start 177; transcript_id "g2.t1"; gene_id "g2"; # coding sequence = [atgatgattgccactctgattagtgtagcgatctatagaagatttctaatgtctcaaccaaaaaagcagaaaaaagaaa # ttatcctctgtacagggaacaaaaacaaactgaaagagttcctgcaaatcctgggaccggactttccataccagattaccaatgaagatgtcgatttg # ccagaatatcaaggtgagccagaagatgttgccagggagaagtgcaagcttgccgctgaacagctgaaatgtccagttatcacagaggacacaagcct # gtgtttcaatgccctgggtggactcccaggcccatacatcaagtggtttctccagaaagtaggacccgaaggtctacacaagatgttggagggctttg # aggataagtctgctacagccatgtgtatcttagcatacagctcaggagagaaagactcggaagtgaaattgttttgtgggaaaacaccaggacagatt # gtgaaaccccgaggacccaatgattttggctgggacccgtgcttccagcccgaggggttcacccagacttacgcagaaatgccaaaagaaaccaaaaa # tacggtttctcacagattcaaagctgtggaactctttaggcaaggaaaacttaatctatag] # protein sequence = [MMIATLISVAIYRRFLMSQPKKQKKEIILCTGNKNKLKEFLQILGPDFPYQITNEDVDLPEYQGEPEDVAREKCKLAA # EQLKCPVITEDTSLCFNALGGLPGPYIKWFLQKVGPEGLHKMLEGFEDKSATAMCILAYSSGEKDSEVKLFCGKTPGQIVKPRGPNDFGWDPCFQPEG # FTQTYAEMPKETKNTVSHRFKAVELFRQGKLNL] # sequence of block unknown_A 23 [KKEIILCTGNK] 34 # sequence of block unknown_B 34 [NKLKEFLQIL] 44 # sequence of block unknown_C 53 [NEDVDLPEYQGEP] 66 # sequence of block unknown_D 70 [REKCKLAAEQLKCPVITEDTSLCFNALGGLPGP] 103 # sequence of block unknown_E 111 [VGPEGLHKMLEGFEDKSATAMCILAYSS] 139 # sequence of block unknown_F 143 [SEVKLFCGKT] 153 # sequence of block unknown_G 156 [IVKPRGPNDFGWDPCFQPE] 175 # sequence of block unknown_H 177 [TQTYAEMPKETKNTVSHRFKAVELFRQGKLN] 208 # end gene g2 ### # start gene g3 Contig30345 AUGUSTUS gene 18874 30105 0.01 - . g3 Contig30345 AUGUSTUS transcript 18874 30105 0.01 - . g3.t1 Contig30345 AUGUSTUS tts 18874 18874 . - . transcript_id "g3.t1"; gene_id "g3"; Contig30345 AUGUSTUS exon 18874 19171 . - . transcript_id "g3.t1"; gene_id "g3"; Contig30345 AUGUSTUS stop_codon 19113 19115 . - 0 transcript_id "g3.t1"; gene_id "g3"; Contig30345 AUGUSTUS intron 19172 19228 0.18 - . transcript_id "g3.t1"; gene_id "g3"; Contig30345 AUGUSTUS intron 19362 19412 0.5 - . transcript_id "g3.t1"; gene_id "g3"; Contig30345 AUGUSTUS intron 19562 20074 1 - . transcript_id "g3.t1"; gene_id "g3"; Contig30345 AUGUSTUS intron 20166 21129 0.97 - . transcript_id "g3.t1"; gene_id "g3"; Contig30345 AUGUSTUS intron 21244 23806 0.26 - . transcript_id "g3.t1"; gene_id "g3"; Contig30345 AUGUSTUS CDS 19113 19171 0.17 - 2 transcript_id "g3.t1"; gene_id "g3"; Contig30345 AUGUSTUS CDS 19229 19361 0.49 - 0 transcript_id "g3.t1"; gene_id "g3"; Contig30345 AUGUSTUS exon 19229 19361 . - . transcript_id "g3.t1"; gene_id "g3"; Contig30345 AUGUSTUS CDS 19413 19561 1 - 2 transcript_id "g3.t1"; gene_id "g3"; Contig30345 AUGUSTUS exon 19413 19561 . - . transcript_id "g3.t1"; gene_id "g3"; Contig30345 AUGUSTUS CDS 20075 20165 1 - 0 transcript_id "g3.t1"; gene_id "g3"; Contig30345 AUGUSTUS exon 20075 20165 . - . transcript_id "g3.t1"; gene_id "g3"; Contig30345 AUGUSTUS CDS 21130 21243 0.93 - 0 transcript_id "g3.t1"; gene_id "g3"; Contig30345 AUGUSTUS exon 21130 21243 . - . transcript_id "g3.t1"; gene_id "g3"; Contig30345 AUGUSTUS CDS 23807 23857 0.31 - 0 transcript_id "g3.t1"; gene_id "g3"; Contig30345 AUGUSTUS exon 23807 23885 . - . transcript_id "g3.t1"; gene_id "g3"; Contig30345 AUGUSTUS start_codon 23855 23857 . - 0 transcript_id "g3.t1"; gene_id "g3"; Contig30345 AUGUSTUS exon 25920 25958 . - . transcript_id "g3.t1"; gene_id "g3"; Contig30345 AUGUSTUS exon 29873 30105 . - . transcript_id "g3.t1"; gene_id "g3"; Contig30345 AUGUSTUS tss 30105 30105 . - . transcript_id "g3.t1"; gene_id "g3"; # coding sequence = [atgaccccgaggaagcttccaaccgtctacataaagccatacagggcttgggatctggtagacgacatatcaggcgacc # tcagtggacattttgaaaaactttgcctctatctgttgatgcccagtagaatgtttgatgcctggtgtctgcatcaggccatggagggccttggaacg # gatgaagaaagactggtagaaattctgtgtggtagaaccaacagcgaaatccattccatcaaagaggaataccaaaattatttcaagaagtccttaga # agatgatgtccgaaaagataccagtggccattttcaacatatcctgatcagcttgctgcagggtaacaggagtgaggagcaggaagtagacaacaaaa # aggtcaaacaagatgcaaaggatctctacgagattaaagcgaggccaactactaaccaaaaattgatgttgcagggttataacgaatctcgtttaaag # tcatcatttcgcaaattctacggtcgctattataatgatcttgtttgcgattacaaatcatcactaaatttgacgacgggtaaccccgtttactttgt # ttcgactacgggctcacggcgggtgtga] # protein sequence = [MTPRKLPTVYIKPYRAWDLVDDISGDLSGHFEKLCLYLLMPSRMFDAWCLHQAMEGLGTDEERLVEILCGRTNSEIHS # IKEEYQNYFKKSLEDDVRKDTSGHFQHILISLLQGNRSEEQEVDNKKVKQDAKDLYEIKARPTTNQKLMLQGYNESRLKSSFRKFYGRYYNDLVCDYK # SSLNLTTGNPVYFVSTTGSRRV] # end gene g3 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370TG2.prfl --predictionStart=0 --predictionEnd=35784 --species=fly ./tmp/Contig3034520180911_busco_2432604931_.temp