[Bioperl-l] quick pairwise alignment

Dave Messina David.Messina at sbc.su.se
Wed Nov 26 18:53:41 EST 2008

Hi Alper,
Great -- glad I was able to help.

is it possible to see the "original" sequence that is used for BLAST in the
> alignment?

Sorry, I can't remember what ClustalW's output looks like. Would you like to
see something like this?


If I were to do it, I think, since you get the start and stop positions of
the hit,  I might try to place the hit string in relation to the query
string. So in the code from before, instead of printing
$hsp_obj->query_string, you could print $input1->seq.

Or, I think if you run blastall outside of BioPerl, there are options for
query-anchored output, but you'd have to parse that out of the blast report

But those are just off the top of my head. Anyone else reading, please chime
in if you've got better ideas.


More information about the Bioperl-l mailing list