# 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 # --[8..57]--> unknown_A (16) <--[0..2]--> unknown_B (33) <--[0..2]--> unknown_C (26) <--[0..25]--> unknown_D (10) <--[6..44]--> unknown_E (19) <--[0..4]--> unknown_F (9) <--[32..63]--> unknown_H (23) <--[8..92]--> unknown_I (11) <--[0..1]--> unknown_J (23) <--[0..19]--> unknown_K (35) <--[3..18]--> unknown_L (17) <--[10..19]--> unknown_N (21) <--[1..22]--> unknown_O (24) <--[0..1]--> unknown_P (25) <--[0..2]--> unknown_Q (30) <--[0..43]-- # BUSCO_20180911_busco_2432604931 version. Using default transition matrix. # admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0) # Looks like ./tmp/Contig17976920180911_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 = 3540, name = Contig179769) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig179769 AUGUSTUS gene 1 3353 0.37 + . g1 Contig179769 AUGUSTUS transcript 1 3353 0.37 + . g1.t1 Contig179769 AUGUSTUS intron 1 339 0.96 + . transcript_id "g1.t1"; gene_id "g1"; Contig179769 AUGUSTUS intron 488 1487 0.94 + . transcript_id "g1.t1"; gene_id "g1"; Contig179769 AUGUSTUS intron 1609 2016 1 + . transcript_id "g1.t1"; gene_id "g1"; Contig179769 AUGUSTUS intron 2124 3242 0.42 + . transcript_id "g1.t1"; gene_id "g1"; Contig179769 AUGUSTUS CDS 340 487 0.98 + 1 transcript_id "g1.t1"; gene_id "g1"; Contig179769 AUGUSTUS CDS 1488 1608 1 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig179769 AUGUSTUS CDS 2017 2123 0.97 + 2 transcript_id "g1.t1"; gene_id "g1"; Contig179769 AUGUSTUS CDS 3243 3353 0.43 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig179769 AUGUSTUS stop_codon 3351 3353 . + 0 transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [attcccaaaatcaggcaatgaagatctggcagtcagcctggcacagtgggtgtttaaggagaaaggcgtcctgcgtgtc # ggtgtagtgaaacacaacaaacaaggggagaaagaaccaccccaggcttacactgtttttgacatggtggaatactcaattggaattgaggaactgaa # ggatggtcagtggaagccatacagtggtcaagatgtccagttagagttcgtccgcattgacccatttgtcagaacaactctgaagaactcaaatggca # agttccatgtcactttcaagctgcccgacgtctatggtgtgtacaagttccaggtggattacaacagagtgggtttcactcacctgtacagcaccaca # cagttgcatgaggtacaatttaaaatgactaaatgtggtaatcgcaccccagacgcttcctccgctgaatctgcccacatgtacactatagagttctg # ccgtcagcattattaa] # protein sequence = [FPKSGNEDLAVSLAQWVFKEKGVLRVGVVKHNKQGEKEPPQAYTVFDMVEYSIGIEELKDGQWKPYSGQDVQLEFVRI # DPFVRTTLKNSNGKFHVTFKLPDVYGVYKFQVDYNRVGFTHLYSTTQLHEVQFKMTKCGNRTPDASSAESAHMYTIEFCRQHY] # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370CTU.prfl --predictionStart=0 --predictionEnd=22231 --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig17976920180911_busco_2432604931_.temp