Question: Can I specify on BLAST (blastp, specifically) the length of subject sequences to align with?
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gravatar for inaciogmedeiros
2.6 years ago by
inaciogmedeiros10 wrote:

Suppose you've got a local BLAST (specifically, blastp) instance and a "fasta reference dataset", and you just wanna align (using blastp) a given query protein sequence against sequences from that dataset whose lengths are the same (or higher) than query's length. Can you set any option when running blastp so that it performs this behavior? If so, which option would be, and how to activate it?

blastp protein alignment • 1.1k views
ADD COMMENTlink modified 2.6 years ago by Elisabeth Gasteiger1.6k • written 2.6 years ago by inaciogmedeiros10
1

why don't you just filter before building the blastdb or filter the blast output ?

ADD REPLYlink written 2.6 years ago by Pierre Lindenbaum119k

I thought this too, and wondered if BLAST could do this "automatically" for me.

ADD REPLYlink written 2.6 years ago by inaciogmedeiros10

Include query length, subject length and alignment length in tabular output and you can do it post blastp with awk with very little effort. blastp -help for how to include this stuff in blast output..

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by 5heikki8.4k
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gravatar for Elisabeth Gasteiger
2.6 years ago by
Geneva
Elisabeth Gasteiger1.6k wrote:

Not exactly what you asked for, but UniProt's BLAST (http://www.uniprot.org/blast) allows you to filter your results in a post-processing step. You can "map to UniProtKB" and then add any search criteria, e.g. sequence length (range), by using the advanced search. However, this just allows you to retrieve/see the sequences, and doesn't maintain the scoring/ranking by BLAST similarity score/e-value etc.

ADD COMMENTlink written 2.6 years ago by Elisabeth Gasteiger1.6k
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