blastp augustus annotation against protein database

Question

[grey]

Hi all. I'm looking for a handy tool to blast amino acid sequence output from Augustus annotation against a protein database to identify the best ortholog. I can imagine doing this with a homemade script but thought there might be a ready made tool out there.

Thanks in advance!

Details:

Augustus output gff looks like this...

# start gene g7
SCF_1   AUGUSTUS        gene    35727   36261   0.01    -       .       g7
SCF_1   AUGUSTUS        transcript      35727   36261   0.01    -       .       g7.t1
SCF_1   AUGUSTUS        tts     35727   35727   .       -       .       transcript_id "g7.t1"; gene_id "g7";
SCF_1   AUGUSTUS        exon    35727   35945   .       -       .       transcript_id "g7.t1"; gene_id "g7";
SCF_1   AUGUSTUS        stop_codon      35907   35909   .       -       0       transcript_id "g7.t1"; gene_id "g7";
SCF_1   AUGUSTUS        intron  35946   36036   0.39    -       .       transcript_id "g7.t1"; gene_id "g7";
SCF_1   AUGUSTUS        CDS     35907   35945   0.39    -       0       transcript_id "g7.t1"; gene_id "g7";
SCF_1   AUGUSTUS        CDS     36037   36228   0.39    -       0       transcript_id "g7.t1"; gene_id "g7";
SCF_1   AUGUSTUS        exon    36037   36261   .       -       .       transcript_id "g7.t1"; gene_id "g7";
SCF_1   AUGUSTUS        start_codon     36226   36228   .       -       0       transcript_id "g7.t1"; gene_id "g7";
SCF_1   AUGUSTUS        tss     36261   36261   .       -       .       transcript_id "g7.t1"; gene_id "g7";
# protein sequence = [MISTASVSGSVDLPRPMKIDSSASPEIESDPTPTSPEGSRTSGSPDRHDPSTSSPSPSRGGDNQNIGNYFVFQLRK]

I want to find the best protein match for the protein sequence at the end.

[lieven.sterck]

if the real issue is how to get to proteins / AA sequence starting from a gff file, I suggest to rephrase your question such that it is clear that's what you want to achieve.

Answer 1

[lieven.sterck]

blast(p) should do the job I think ?