[BiO BB] Building an alignment from BLAST hsp

[Gary Van Domselaar]

Hi Ryan,

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:
http://www.bioperl.org/wiki/HOWTO:SearchIO

to grab the coordinates and sequences from the alignments and then use the 
Bio::SimpleAlign module: 
http://doc.bioperl.org/releases/bioperl-1.5.0-RC1/Bio/SimpleAlign.html

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?
>
> Ryan
>
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-- 
Gary Van Domselaar, PhD
Associate Director, Bioinformatics.Org
gary at bioinformatics.org