[EMBOSS] Building an alignment from BLAST hsp

Ryan Golhar golharam at umdnj.edu
Mon Mar 27 16:50:42 UTC 2006

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?


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