# 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 # --[4..781]--> unknown_A (28) <--[0..1]--> unknown_B (20) <--[2..21]--> unknown_C (39) <--[1..51]--> unknown_D (28) <--[0..2]--> unknown_E (11) <--[6..21]--> unknown_F (14) <--[6..28]--> unknown_G (30) <--[0..1150]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig5285320180911_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 = 9582, name = Contig52853) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig52853 AUGUSTUS gene 778 9169 0.01 + . g1 Contig52853 AUGUSTUS transcript 778 9169 0.01 + . g1.t1 Contig52853 AUGUSTUS exon 778 965 . + . transcript_id "g1.t1"; gene_id "g1"; Contig52853 AUGUSTUS start_codon 879 881 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig52853 AUGUSTUS intron 966 3400 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig52853 AUGUSTUS intron 3548 4480 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig52853 AUGUSTUS intron 4535 4656 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig52853 AUGUSTUS intron 4755 6030 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig52853 AUGUSTUS intron 6120 6281 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig52853 AUGUSTUS intron 6373 7662 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig52853 AUGUSTUS CDS 879 965 0.04 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig52853 AUGUSTUS CDS 3401 3547 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig52853 AUGUSTUS exon 3401 3547 . + . transcript_id "g1.t1"; gene_id "g1"; Contig52853 AUGUSTUS CDS 4481 4534 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig52853 AUGUSTUS exon 4481 4534 . + . transcript_id "g1.t1"; gene_id "g1"; Contig52853 AUGUSTUS CDS 4657 4754 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig52853 AUGUSTUS exon 4657 4754 . + . transcript_id "g1.t1"; gene_id "g1"; Contig52853 AUGUSTUS CDS 6031 6119 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig52853 AUGUSTUS exon 6031 6119 . + . transcript_id "g1.t1"; gene_id "g1"; Contig52853 AUGUSTUS CDS 6282 6372 0.01 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig52853 AUGUSTUS exon 6282 6372 . + . transcript_id "g1.t1"; gene_id "g1"; Contig52853 AUGUSTUS CDS 7663 7759 0.01 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig52853 AUGUSTUS exon 7663 7777 . + . transcript_id "g1.t1"; gene_id "g1"; Contig52853 AUGUSTUS stop_codon 7757 7759 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig52853 AUGUSTUS exon 9078 9169 . + . transcript_id "g1.t1"; gene_id "g1"; Contig52853 AUGUSTUS tts 9169 9169 . + . transcript_id "g1.t1"; gene_id "g1"; Contig52853 AUGUSTUS protein_match 930 965 2.84 + 0 target "unknown_A[1..12]"; target_start 17; transcript_id "g1.t1"; gene_id "g1"; Contig52853 AUGUSTUS protein_match 3401 3448 5.36 + 0 target "unknown_A[13..28]"; target_start 17; transcript_id "g1.t1"; gene_id "g1"; Contig52853 AUGUSTUS protein_match 3449 3508 4.12 + 0 target "unknown_B[1..20]"; target_start 45; transcript_id "g1.t1"; gene_id "g1"; Contig52853 AUGUSTUS protein_match 3515 3547 5.12 + 0 target "unknown_C[1..11]"; target_start 67; transcript_id "g1.t1"; gene_id "g1"; Contig52853 AUGUSTUS protein_match 4481 4534 7.07 + 2 target "unknown_C[12..30]"; target_start 66; transcript_id "g1.t1"; gene_id "g1"; Contig52853 AUGUSTUS protein_match 4657 4686 3.89 + 0 target "unknown_C[30..39]"; target_start 67; transcript_id "g1.t1"; gene_id "g1"; Contig52853 AUGUSTUS protein_match 4708 4754 3.3 + 0 target "unknown_D[1..16]"; target_start 113; transcript_id "g1.t1"; gene_id "g1"; Contig52853 AUGUSTUS protein_match 6031 6067 2.5 + 1 target "unknown_D[16..28]"; target_start 113; transcript_id "g1.t1"; gene_id "g1"; Contig52853 AUGUSTUS protein_match 6074 6106 4.77 + 0 target "unknown_E[1..11]"; target_start 143; transcript_id "g1.t1"; gene_id "g1"; Contig52853 AUGUSTUS protein_match 6296 6337 4.03 + 0 target "unknown_F[1..14]"; target_start 163; transcript_id "g1.t1"; gene_id "g1"; Contig52853 AUGUSTUS protein_match 7667 7756 2.98 + 0 target "unknown_G[1..30]"; target_start 190; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atggcagatattgatgaagttgatggtgctagcgatgaagaagttgaggcattgacagctggtgaagtacttcaaaagc # tggaggaggcctggctaaatgagaaattttctcctgagttattggaggcaaagacagatttagttgactgcatgttggaacaaatgacagaaatggaa # gaaaacatcaagcgagcaaagaaaggagacttcaaagttgtgctgcatagaatggagatagacaggataagatatgtactgagcagttaccttagatg # taggttgaaaaagatagagaaatacacagttcataccttggagcaggagagcaaccgacaggatgaagatgtctgtcgtctgtcaccagaggagttca # cattcgctaaagaatatgcagccacattggaaacacatatgaagaatttgggtctccggcacatgcctcctaatttacagacaatggatccaaaacaa # acaacaatccgtcccaacctggacagctacgttttcttgagagtgaacgaagacactgatggagttttggtggaggaagagacactagacacagggga # agaaattgtggatttacaaaagggggaccaacacataatgcgatacaaacctctctcagctttagtgatatcaggagctgtaacgctgatatga] # protein sequence = [MADIDEVDGASDEEVEALTAGEVLQKLEEAWLNEKFSPELLEAKTDLVDCMLEQMTEMEENIKRAKKGDFKVVLHRME # IDRIRYVLSSYLRCRLKKIEKYTVHTLEQESNRQDEDVCRLSPEEFTFAKEYAATLETHMKNLGLRHMPPNLQTMDPKQTTIRPNLDSYVFLRVNEDT # DGVLVEEETLDTGEEIVDLQKGDQHIMRYKPLSALVISGAVTLI] # sequence of block unknown_A 17 [LTAGEVLQKLEEAWLNEKFSPELLEAKT] 45 # sequence of block unknown_B 45 [DLVDCMLEQMTEMEENIKRA] 65 # sequence of block unknown_C 67 [GDFKVVLHRMEIDRIRYVLSSYLRCRLKKIEKYTVHTLE] 106 # sequence of block unknown_D 113 [EDVCRLSPEEFTFAKEYAATLETHMKNL] 141 # sequence of block unknown_E 143 [RHMPPNLQTMD] 154 # sequence of block unknown_F 163 [LDSYVFLRVNEDTD] 177 # sequence of block unknown_G 190 [EIVDLQKGDQHIMRYKPLSALVISGAVTLI] 220 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370WZX.prfl --predictionStart=0 --predictionEnd=23550 --species=fly ./tmp/Contig5285320180911_busco_2432604931_.temp