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

Catherine Letondal letondal at pasteur.fr
Tue Mar 28 07:25:07 UTC 2006

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:

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


Catherine Letondal -- Institut Pasteur -- Computing Center

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