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

[Catherine Letondal]

On Mar 27, 2006, at 8:03 PM, Ryan Golhar wrote:

> Hi Peter,
>
>> 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 solution.
>
> I looked at a bioperl method, but can't seem to find something that 
> will
> accomplish this.
>
>> 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.
>
> Yes, I agree.  I suppose the best way would be to specify the two
> sequences and the blast output.  The application could then construct 
> an
> alignment based on a particular HSP (probably the first one, or 
> whatever
> the user specifies).
>

Have you tried this:
http://bioweb.pasteur.fr/seqanal/interfaces/seqsblast.html

It is based on bioperl. check "Get HSP" option (you can even extend it).

Best,

--
Catherine Letondal -- Institut Pasteur -- Computing Center