Question: blastp augustus annotation against protein database
0
gravatar for Grey Monroe
3 months ago by
Grey Monroe10
Max Planck Institute
Grey Monroe10 wrote:

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.

blast annotation augustus • 116 views
ADD COMMENTlink modified 3 months ago by lieven.sterck6.9k • written 3 months ago by Grey Monroe10
1

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.

ADD REPLYlink written 3 months ago by lieven.sterck6.9k
1
gravatar for lieven.sterck
3 months ago by
lieven.sterck6.9k
VIB, Ghent, Belgium
lieven.sterck6.9k wrote:

blast(p) should do the job I think ?

ADD COMMENTlink modified 3 months ago • written 3 months ago by lieven.sterck6.9k
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