[BiO BB] Building an alignment from BLAST hsp

Ryan Golhar golharam at umdnj.edu
Mon Mar 27 13:03:39 EST 2006

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).


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