[BiO BB] Building an alignment from BLAST hsp

Gary Van Domselaar gary at primary.bioinformatics.org
Mon Mar 27 12:09:12 EST 2006

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:

to grab the coordinates and sequences from the alignments and then use the 
Bio::SimpleAlign module: 

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
> _______________________________________________
> Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board

Gary Van Domselaar, PhD
Associate Director, Bioinformatics.Org
gary at bioinformatics.org

More information about the BBB mailing list