Can I specify on BLAST (blastp, specifically) the length of subject sequences to align with?

Question

[inaciogmedeiros]

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?

[Pierre Lindenbaum]

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

[inaciogmedeiros]

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

[5heikki]

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..

Answer 1

[Elisabeth Gasteiger]

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.