# 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 # --[32..221]--> unknown_D (9) <--[0..1]--> unknown_E (14) <--[1..39]--> unknown_F (47) <--[1..13]--> unknown_G (18) <--[1..38]--> unknown_H (18) <--[1..28]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig5302520180911_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 = 24987, name = Contig53025) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig53025 AUGUSTUS gene 1759 4595 0.03 - . g1 Contig53025 AUGUSTUS transcript 1759 4595 0.03 - . g1.t1 Contig53025 AUGUSTUS tts 1759 1759 . - . transcript_id "g1.t1"; gene_id "g1"; Contig53025 AUGUSTUS exon 1759 2355 . - . transcript_id "g1.t1"; gene_id "g1"; Contig53025 AUGUSTUS stop_codon 2113 2115 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig53025 AUGUSTUS intron 2356 3986 0.97 - . transcript_id "g1.t1"; gene_id "g1"; Contig53025 AUGUSTUS CDS 2113 2355 0.95 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig53025 AUGUSTUS CDS 3987 4205 1 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig53025 AUGUSTUS exon 3987 4230 . - . transcript_id "g1.t1"; gene_id "g1"; Contig53025 AUGUSTUS start_codon 4203 4205 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig53025 AUGUSTUS exon 4497 4595 . - . transcript_id "g1.t1"; gene_id "g1"; Contig53025 AUGUSTUS tss 4595 4595 . - . transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgcaggagggatgtatcatccttattctggctgttctgacatgtctcaacttctatggatctgatggtttggtggttt # cgccgcggtggtattcgccagggcggacggactttgttttggaccacaagttctacaactacctgggtacagttcatttcacttacttaaagattaga # ttgatttcaaatacagtttgttcccacgtcaagcagtacccggaatgcaagatccagatcaaggggaagacggaggagattgaaaagaggaaggagtc # gcagaagaagacggaatcagcgaagaagacgaagacggcttcagagaagaagacgaagacgaacccagagaagaagacgaagacggattcagagaaaa # agacggcgggtttacagaaaagaacggttttacagaagaaggtggagtcagaggagaggaaaggttcacagaagacggcacggccatag] # protein sequence = [MQEGCIILILAVLTCLNFYGSDGLVVSPRWYSPGRTDFVLDHKFYNYLGTVHFTYLKIRLISNTVCSHVKQYPECKIQ # IKGKTEEIEKRKESQKKTESAKKTKTASEKKTKTNPEKKTKTDSEKKTAGLQKRTVLQKKVESEERKGSQKTARP] # end gene g1 ### # start gene g2 Contig53025 AUGUSTUS gene 17098 24915 0.01 - . g2 Contig53025 AUGUSTUS transcript 17098 24915 0.01 - . g2.t1 Contig53025 AUGUSTUS tts 17098 17098 . - . transcript_id "g2.t1"; gene_id "g2"; Contig53025 AUGUSTUS exon 17098 17569 . - . transcript_id "g2.t1"; gene_id "g2"; Contig53025 AUGUSTUS stop_codon 17433 17435 . - 0 transcript_id "g2.t1"; gene_id "g2"; Contig53025 AUGUSTUS intron 17570 17919 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig53025 AUGUSTUS intron 18157 19646 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig53025 AUGUSTUS intron 19681 20972 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig53025 AUGUSTUS intron 20995 21345 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig53025 AUGUSTUS intron 21379 21469 0.01 - . transcript_id "g2.t1"; gene_id "g2"; Contig53025 AUGUSTUS CDS 17433 17569 0.01 - 2 transcript_id "g2.t1"; gene_id "g2"; Contig53025 AUGUSTUS CDS 17920 18156 0.01 - 2 transcript_id "g2.t1"; gene_id "g2"; Contig53025 AUGUSTUS exon 17920 18156 . - . transcript_id "g2.t1"; gene_id "g2"; Contig53025 AUGUSTUS CDS 19647 19680 0.01 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig53025 AUGUSTUS exon 19647 19680 . - . transcript_id "g2.t1"; gene_id "g2"; Contig53025 AUGUSTUS CDS 20973 20994 0.01 - 1 transcript_id "g2.t1"; gene_id "g2"; Contig53025 AUGUSTUS exon 20973 20994 . - . transcript_id "g2.t1"; gene_id "g2"; Contig53025 AUGUSTUS CDS 21346 21378 0.01 - 1 transcript_id "g2.t1"; gene_id "g2"; Contig53025 AUGUSTUS exon 21346 21378 . - . transcript_id "g2.t1"; gene_id "g2"; Contig53025 AUGUSTUS CDS 21470 21528 0.01 - 0 transcript_id "g2.t1"; gene_id "g2"; Contig53025 AUGUSTUS exon 21470 21546 . - . transcript_id "g2.t1"; gene_id "g2"; Contig53025 AUGUSTUS start_codon 21526 21528 . - 0 transcript_id "g2.t1"; gene_id "g2"; Contig53025 AUGUSTUS exon 24505 24915 . - . transcript_id "g2.t1"; gene_id "g2"; Contig53025 AUGUSTUS tss 24915 24915 . - . transcript_id "g2.t1"; gene_id "g2"; Contig53025 AUGUSTUS protein_match 17472 17525 1.91 - 0 target "unknown_H[1..18]"; target_start 143; transcript_id "g2.t1"; gene_id "g2"; Contig53025 AUGUSTUS protein_match 17529 17569 4.93 - 2 target "unknown_G[5..18]"; target_start 124; transcript_id "g2.t1"; gene_id "g2"; Contig53025 AUGUSTUS protein_match 17920 17932 5.24 - 0 target "unknown_G[1..5]"; target_start 124; transcript_id "g2.t1"; gene_id "g2"; Contig53025 AUGUSTUS protein_match 17936 18076 3.86 - 0 target "unknown_F[1..47]"; target_start 76; transcript_id "g2.t1"; gene_id "g2"; Contig53025 AUGUSTUS protein_match 18125 18156 1.25 - 2 target "unknown_E[4..14]"; target_start 46; transcript_id "g2.t1"; gene_id "g2"; Contig53025 AUGUSTUS protein_match 19647 19656 1.42 - 0 target "unknown_E[1..4]"; target_start 46; transcript_id "g2.t1"; gene_id "g2"; Contig53025 AUGUSTUS protein_match 19657 19680 1.42 - 0 target "unknown_D[2..9]"; target_start 37; transcript_id "g2.t1"; gene_id "g2"; Contig53025 AUGUSTUS protein_match 20973 20975 4.63 - 0 target "unknown_D[1..1]"; target_start 37; transcript_id "g2.t1"; gene_id "g2"; # coding sequence = [atgcatgacttatggaaggactacaatgagggcaagcgttggttaacagataaaatcaaatcaaacttaaacgttggta # caagtcatcctagctcacctgagcctaaggctcaaatgtaccaagtttacgttttcatgcactgtcagtatttatcacaatttacaaattatttacac # attgttgatatgactataacaagactattattctttttcagaacctttgatcagtttaaatgtgacagtattctaaaagcagatttccatgggtgctt # tttaacagtatcaaagtcatgttgtccttcatacattggttctactggcatcgtcattatggaaacaaagaacacattcaaaatcatcaccaaacaaa # atcgtattaaatgtattccaaaaagaaacagtgtttttatgtttgaactagatggacactatataactgtgtatggaaataatttctgttgtcatcta # gtattgagatcaacatataaatttaaaccaaagaaatatgttgcaatatga] # protein sequence = [MHDLWKDYNEGKRWLTDKIKSNLNVGTSHPSSPEPKAQMYQVYVFMHCQYLSQFTNYLHIVDMTITRLLFFFRTFDQF # KCDSILKADFHGCFLTVSKSCCPSYIGSTGIVIMETKNTFKIITKQNRIKCIPKRNSVFMFELDGHYITVYGNNFCCHLVLRSTYKFKPKKYVAI] # sequence of block unknown_H 143 [HYITVYGNNFCCHLVLRS] 161 # sequence of block unknown_G 124 [NRIKCIPKRNSVFMFELD] 142 # sequence of block unknown_F 76 [QFKCDSILKADFHGCFLTVSKSCCPSYIGSTGIVIMETKNTFKIITK] 123 # sequence of block unknown_E 46 [HCQYLSQFTNYLHI] 60 # sequence of block unknown_D 37 [QMYQVYVFM] 46 # end gene g2 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370QT3.prfl --predictionStart=0 --predictionEnd=38058 --species=fly ./tmp/Contig5302520180911_busco_2432604931_.temp