# 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..81]--> unknown_A (38) <--[2..37]--> unknown_B (29) <--[1..47]--> unknown_C (46) <--[0..3]--> unknown_D (12) <--[8..51]--> unknown_E (46) <--[5..39]--> unknown_F (90) <--[0..24]--> unknown_G (12) <--[0..91]--> unknown_H (34) <--[0..1]--> unknown_I (14) <--[0..11]-- # fly version. Using default transition matrix. # Looks like ./tmp/Contig1520180911_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 = 37367, name = Contig15) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig15 AUGUSTUS gene 13871 21315 0.01 - . g1 Contig15 AUGUSTUS transcript 13871 21315 0.01 - . g1.t1 Contig15 AUGUSTUS tts 13871 13871 . - . transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS exon 13871 15109 . - . transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS stop_codon 15047 15049 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS intron 15110 16683 0.01 - . transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS intron 16928 17179 0.95 - . transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS intron 17369 19049 0.02 - . transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS intron 19135 19926 0.02 - . transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS intron 20074 20187 0.98 - . transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS intron 20402 20741 0.88 - . transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS intron 20866 21014 0.65 - . transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS intron 21174 21237 0.04 - . transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS CDS 15047 15109 0.01 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS CDS 16684 16927 0.75 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS exon 16684 16927 . - . transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS CDS 17180 17368 0.86 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS exon 17180 17368 . - . transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS CDS 19050 19134 0.02 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS exon 19050 19134 . - . transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS CDS 19927 20073 0.98 - 2 transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS exon 19927 20073 . - . transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS CDS 20188 20401 0.88 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS exon 20188 20401 . - . transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS CDS 20742 20865 0.68 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS exon 20742 20865 . - . transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS CDS 21015 21173 0.04 - 1 transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS exon 21015 21173 . - . transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS CDS 21238 21269 0.04 - 0 transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS exon 21238 21315 . - . transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS start_codon 21267 21269 . - 0 transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS tss 21315 21315 . - . transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS protein_match 15053 15094 3.62 - 0 target "unknown_I[1..14]"; target_start 403; transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS protein_match 15095 15109 4.66 - 0 target "unknown_H[30..34]"; target_start 369; transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS protein_match 16684 16770 4.55 - 0 target "unknown_H[1..29]"; target_start 369; transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS protein_match 16894 16927 2.93 - 1 target "unknown_G[1..12]"; target_start 316; transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS protein_match 17180 17181 1 - 0 target "unknown_G[1..1]"; target_start 316; transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS protein_match 17182 17368 10.6 - 1 target "unknown_F[28..90]"; target_start 226; transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS protein_match 19050 19132 4.28 - 0 target "unknown_F[1..28]"; target_start 226; transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS protein_match 19940 20073 7.73 - 2 target "unknown_E[2..46]"; target_start 175; transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS protein_match 20188 20191 6.63 - 0 target "unknown_E[1..2]"; target_start 175; transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS protein_match 20216 20251 5.04 - 0 target "unknown_D[1..12]"; target_start 155; transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS protein_match 20261 20398 7.7 - 0 target "unknown_C[1..46]"; target_start 106; transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS protein_match 20784 20865 6.17 - 1 target "unknown_B[2..29]"; target_start 62; transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS protein_match 21015 21019 3.35 - 0 target "unknown_B[1..2]"; target_start 62; transcript_id "g1.t1"; gene_id "g1"; Contig15 AUGUSTUS protein_match 21026 21139 3.72 - 0 target "unknown_A[1..38]"; target_start 22; transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atgaaagtacgttacgtatcatctcgcgagagtatggagttgtctgacacgcagattcatattcttgtaaacgctggga # tgtcaaccttgggcttttttgtttgctacaacatcatcccaaagttcagagccatgtttatcaatgcgcacctctttggaatagacatgagtaaacga # gaaaagataaaaatcccggaatctcaaggaatgatatgcggtgccatttttctggttattatgtttctgtttatcccagtgccattttacaagcatat # tgtgacagacaatttggcaaattctttcccacatcatgagtacatagaatacatagcagccttgctgtccatatgctgcatgatatttttgggatttg # ctgatgatgtcttggagcttaagtggagacacaaactgtttttaccaaccatggcatcattaccattgttaatggtgtacttggttaactttgactca # actgttataatcgttcctaaacccctgcgcttttatttgggtcacgatgtagatttaggaatattgtactatgtttatatgggaatgttggctgtatt # ttgcaccaatgctatcaacattttgtcgggagtgaatggattggaaacaggacaatctctgatcattgccctgtctgtacttatttttaatttcattg # aactgaatgggtgttgcagagaagcacatgtcttcagcatatatttcattttaccatacaccgctgtatgcttggccatttttatacacaactggtac # ccggccgatgtctttgtgggagacaccttctgctatttctcaggaatgacatttgcagtagtggcaattttagggcactttagcaaaactatgttact # cttttttataccccaagtcttcaattttatatactctgtaccccagctttttaaaatggtgccatgtccaagacatcgattgcccagatatgacccaa # caagtgacacagtacgaatgagtacaacaacctttaagtatcagaatttaaacgttctgggaaagctttccgtgacggtgttcaggatgctgttcctg # ctggacgtgacggagggcgtgggagaggagaaccagctaatggagtgtaataacatgactctcgtaaacctgatcctcaaattctgcggacctctgca # tgaaaagaccctagtcaccatcctgttaacaatacaggttttttgcagtgtacttgcatttgggataaggtaccaactgtccaaggttttttacgatt # aa] # protein sequence = [MKVRYVSSRESMELSDTQIHILVNAGMSTLGFFVCYNIIPKFRAMFINAHLFGIDMSKREKIKIPESQGMICGAIFLV # IMFLFIPVPFYKHIVTDNLANSFPHHEYIEYIAALLSICCMIFLGFADDVLELKWRHKLFLPTMASLPLLMVYLVNFDSTVIIVPKPLRFYLGHDVDL # GILYYVYMGMLAVFCTNAINILSGVNGLETGQSLIIALSVLIFNFIELNGCCREAHVFSIYFILPYTAVCLAIFIHNWYPADVFVGDTFCYFSGMTFA # VVAILGHFSKTMLLFFIPQVFNFIYSVPQLFKMVPCPRHRLPRYDPTSDTVRMSTTTFKYQNLNVLGKLSVTVFRMLFLLDVTEGVGEENQLMECNNM # TLVNLILKFCGPLHEKTLVTILLTIQVFCSVLAFGIRYQLSKVFYD] # sequence of block unknown_I 403 [LAFGIRYQLSKVFY] 417 # sequence of block unknown_H 369 [NNMTLVNLILKFCGPLHEKTLVTILLTIQVFCSV] 403 # sequence of block unknown_G 316 [RYDPTSDTVRMS] 328 # sequence of block unknown_F 226 [CCREAHVFSIYFILPYTAVCLAIFIHNWYPADVFVGDTFCYFSGMTFAVVAILGHFSKTMLLFFIPQVFNFIYSVPQLFKMVPCPRHRLP] 316 # sequence of block unknown_E 175 [LGILYYVYMGMLAVFCTNAINILSGVNGLETGQSLIIALSVLIFNF] 221 # sequence of block unknown_D 155 [DSTVIIVPKPLR] 167 # sequence of block unknown_C 106 [IEYIAALLSICCMIFLGFADDVLELKWRHKLFLPTMASLPLLMVYL] 152 # sequence of block unknown_B 62 [KIPESQGMICGAIFLVIMFLFIPVPFYKH] 91 # sequence of block unknown_A 22 [VNAGMSTLGFFVCYNIIPKFRAMFINAHLFGIDMSKRE] 60 # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370HD7.prfl --predictionStart=0 --predictionEnd=37367 --species=fly ./tmp/Contig1520180911_busco_2432604931_.temp