[BiO BB] Building an alignment from BLAST hsp
Gary Van Domselaar
gary at primary.bioinformatics.org
Mon Mar 27 12:09:12 EST 2006
The BLAST output will have the coordinates of the HSP for your query and
database sequence. You can pretty easily write a script using bioperl's
BLAST parsing modules:
to grab the coordinates and sequences from the alignments and then use the
to remap the query on to the full database sequence.
On Mon, 27 Mar 2006, Ryan Golhar wrote:
> I have a BLAST alignment: query sequence and database sequence.
> The alignment is only showing the HSP from the blast output as expected,
> however I want to build an alignment of the entire database sequence
> against my query sequence.
> I tried using needle from EMBOSS, however its aligning the sequences
> completely different than BLAST does. What I'd really like is a way to
> anchor the alignment based on the BLAST HSP. Does anyone know how to do
> this, or what tool(s) will allow me to do this?
> Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org
Gary Van Domselaar, PhD
Associate Director, Bioinformatics.Org
gary at bioinformatics.org
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