[EMBOSS] [BiO BB] Building an alignment from BLAST hsp

pmr at ebi.ac.uk pmr at ebi.ac.uk
Mon Mar 27 17:50:09 UTC 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?

You are quite right that EMBOSS may align the sequences completely
differently - unless the HSPs are very significant and cover most of the
sequence this will be true of any attempt to simply realign. There has to
be some way to pass on the HSPs as fixed positions, as in the BioPerl

However, it could make a nice EMBOSS application - the only question would
be how you would like to specify the HSPs. Perhaps we could read BLAST
output (in some specified format), or perhaps some other way to give the
input alignments.

We do have at least one EMBOSS application that does something similar
(finds all long perfect matches and interpolates) - we just need to reuse
the interpolation code which is basically doing a global alignment of the
bits in between. That also tackles the problem of choosing which
non-compatible initial matches to use.

Hope that helps,


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