# 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..140]--> unknown_A (23) <--[0..2]--> unknown_B (80) <--[1..9]--> unknown_C (40) <--[1..7]--> unknown_D (28) <--[0..11]--> unknown_E (15) <--[2..7]--> unknown_F (13) <--[0..2]--> unknown_G (44) <--[33..124]--> unknown_I (32) <--[10..20]--> unknown_K (18) <--[0..32]--> unknown_L (44) <--[23..168]--> unknown_O (54) <--[0..39]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig1923420180911_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 = 1774, name = Contig19234) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig19234 AUGUSTUS gene 2 1774 0.01 + . g1 Contig19234 AUGUSTUS transcript 2 1774 0.01 + . g1.t1 Contig19234 AUGUSTUS start_codon 2 4 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig19234 AUGUSTUS intron 1271 1334 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig19234 AUGUSTUS intron 1369 1500 0.01 + . transcript_id "g1.t1"; gene_id "g1"; Contig19234 AUGUSTUS CDS 2 1270 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig19234 AUGUSTUS exon 2 1270 . + . transcript_id "g1.t1"; gene_id "g1"; Contig19234 AUGUSTUS CDS 1335 1368 0.01 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig19234 AUGUSTUS exon 1335 1368 . + . transcript_id "g1.t1"; gene_id "g1"; Contig19234 AUGUSTUS CDS 1501 1766 0.05 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig19234 AUGUSTUS exon 1501 1774 . + . transcript_id "g1.t1"; gene_id "g1"; Contig19234 AUGUSTUS stop_codon 1764 1766 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig19234 AUGUSTUS tts 1774 1774 . + . transcript_id "g1.t1"; gene_id "g1"; Contig19234 AUGUSTUS protein_match 14 82 3.77 + 0 target "unknown_A[1..23]"; target_start 4; transcript_id "g1.t1"; gene_id "g1"; Contig19234 AUGUSTUS protein_match 89 328 5.8 + 0 target "unknown_B[1..80]"; target_start 29; transcript_id "g1.t1"; gene_id "g1"; Contig19234 AUGUSTUS protein_match 332 451 7.04 + 0 target "unknown_C[1..40]"; target_start 110; transcript_id "g1.t1"; gene_id "g1"; Contig19234 AUGUSTUS protein_match 458 541 4.55 + 0 target "unknown_D[1..28]"; target_start 152; transcript_id "g1.t1"; gene_id "g1"; Contig19234 AUGUSTUS protein_match 542 586 10.3 + 0 target "unknown_E[1..15]"; target_start 180; transcript_id "g1.t1"; gene_id "g1"; Contig19234 AUGUSTUS protein_match 593 631 3.31 + 0 target "unknown_F[1..13]"; target_start 197; transcript_id "g1.t1"; gene_id "g1"; Contig19234 AUGUSTUS protein_match 632 763 6.49 + 0 target "unknown_G[1..44]"; target_start 210; transcript_id "g1.t1"; gene_id "g1"; Contig19234 AUGUSTUS protein_match 956 1051 5.78 + 0 target "unknown_I[1..32]"; target_start 318; transcript_id "g1.t1"; gene_id "g1"; Contig19234 AUGUSTUS protein_match 1091 1144 5.13 + 0 target "unknown_K[1..18]"; target_start 363; transcript_id "g1.t1"; gene_id "g1"; Contig19234 AUGUSTUS protein_match 1148 1270 7.08 + 0 target "unknown_L[1..41]"; target_start 382; transcript_id "g1.t1"; gene_id "g1"; Contig19234 AUGUSTUS protein_match 1335 1343 1.38 + 0 target "unknown_L[42..44]"; target_start 382; transcript_id "g1.t1"; gene_id "g1"; Contig19234 AUGUSTUS protein_match 1572 1733 3.88 + 0 target "unknown_O[1..54]"; target_start 458; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgggagggcagcgacaaaagaagtatgaaaagggagaagccacggcatttatgtccagaaaccaagcagtcagcaaac # tgcagctaacacttgcagatttcagacgcttatgcattttgaaaggaatttatccacatgaacccaaccacaagaagagggtaaacaaaggaagcaca # gttcccaagacatactacctggtcaaggacatcaactttctagcgcatgaacctatcattaacaagttcagggagttcaagcactttgtgaggagatt # gaagaaagcaatcaataaaagaaacaaagatgcagaacagagaattcgcagcaataaacccaagtacaagctggatcacattgtcaaggaaaggtatc # cctcattccaagatgctctgagcgacttggatgactgcctgtccatgtgttttctgtttggaacaatgccacagagtgcacggatacacatggaatac # atcaaccatgccagaaaactcacagtggagttcatgcattacatcatagcatcaaggtcattaagaaaggtgttcatttccataaaagggatatacta # ccaagcagaggtgatgggacagacgctaacttgggtgatgcctcacagccttgggtttcagcatccagaagatgtggactacaaagtaatgcagacgt # ttgtggaattttacacaacattactgggattcataaattacaagttgtaccacagcatcaatctacactacccaccaaagctagagctggagatggct # gatgtaagtgaggaaaaaatgacagaaaaggaaagatatcaggagaggttgtccgccttgtctcagacattgaggtctctagatgaaggaggtggtga # agatgaggttcacttagatgaatttccagtctctgatgctgatgacccagatcgagttgagaaagcgaaagttgaagcagagaaagtgaagaagttac # agaacttgtttaaaggacagaaatttttcctgaacagggaagttcctagagaaacattagtttttatcatcaggtgctttggaggtgaagtgtcttgg # catgagtcagttgctgtaggagccactttccccgagtcagatgagtctataacacatcagatagtggacagacctcaagcaaacaaccagtatctgtc # taggtactatgtacagcctcagtgggtgtttgacagtgtgaatgcaaactctctagtccctgtagagcactactttcctggagccaccctccctcctc # atctgtccccatttgatgattcgggtgtgaaagagattgaagaagaaactgctgataactcaaagaagctgaacatgtcagtagaagctggagctgca # gagaaagtcaacgtggagcaaaaactccagcgacagacaatggaggagcgcagactggcagaaatgatgatccccaagaaaaagaaacgactgtatga # taaaatcatgtatgccaaaaaaaagaaaacccaagagacaagaaaattgaaggaaaaacgtgaggcaatagagaaacaaaagaaagccggtggtagta # agaagaagaaaaaagtgtga] # protein sequence = [MGGQRQKKYEKGEATAFMSRNQAVSKLQLTLADFRRLCILKGIYPHEPNHKKRVNKGSTVPKTYYLVKDINFLAHEPI # INKFREFKHFVRRLKKAINKRNKDAEQRIRSNKPKYKLDHIVKERYPSFQDALSDLDDCLSMCFLFGTMPQSARIHMEYINHARKLTVEFMHYIIASR # SLRKVFISIKGIYYQAEVMGQTLTWVMPHSLGFQHPEDVDYKVMQTFVEFYTTLLGFINYKLYHSINLHYPPKLELEMADVSEEKMTEKERYQERLSA # LSQTLRSLDEGGGEDEVHLDEFPVSDADDPDRVEKAKVEAEKVKKLQNLFKGQKFFLNREVPRETLVFIIRCFGGEVSWHESVAVGATFPESDESITH # QIVDRPQANNQYLSRYYVQPQWVFDSVNANSLVPVEHYFPGATLPPHLSPFDDSGVKEIEEETADNSKKLNMSVEAGAAEKVNVEQKLQRQTMEERRL # AEMMIPKKKKRLYDKIMYAKKKKTQETRKLKEKREAIEKQKKAGGSKKKKKV] # sequence of block unknown_A 4 [RQKKYEKGEATAFMSRNQAVSKL] 27 # sequence of block unknown_B 29 [TLADFRRLCILKGIYPHEPNHKKRVNKGSTVPKTYYLVKDINFLAHEPIINKFREFKHFVRRLKKAINKRNKDAEQRIRS] 109 # sequence of block unknown_C 110 [KPKYKLDHIVKERYPSFQDALSDLDDCLSMCFLFGTMPQS] 150 # sequence of block unknown_D 152 [IHMEYINHARKLTVEFMHYIIASRSLRK] 180 # sequence of block unknown_E 180 [VFISIKGIYYQAEVM] 195 # sequence of block unknown_F 197 [TLTWVMPHSLGFQ] 210 # sequence of block unknown_G 210 [HPEDVDYKVMQTFVEFYTTLLGFINYKLYHSINLHYPPKLELEM] 254 # sequence of block unknown_I 318 [KLQNLFKGQKFFLNREVPRETLVFIIRCFGGE] 350 # sequence of block unknown_K 363 [PESDESITHQIVDRPQAN] 381 # sequence of block unknown_L 382 [QYLSRYYVQPQWVFDSVNANSLVPVEHYFPGATLPPHLSPFDDS] 426 # sequence of block unknown_O 458 [KLQRQTMEERRLAEMMIPKKKKRLYDKIMYAKKKKTQETRKLKEKREAIEKQKK] 512 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093708IM.prfl --predictionStart=0 --predictionEnd=21273 --species=fly ./tmp/Contig1923420180911_busco_2432604931_.temp