[Bioperl-l] HSPs: getting the location of mismatch

[Jason Stajich]

Bio::Search::HSP::HSPI objects can do this:
 (Although the docs don't explicitly say this)
my @gappositions = $hsp->seq_inds('query','gap')

Gets the gaps in the query sequence

If you wanted the inserts in the hit seq we'd have to do some more
arithmitic.  Seems like a place for an addition to the HSP object.


We could also do withs someone adding a function to Bio::SimpleAlign which
reports the gapped columns (we already have one which removes them).

Volunteers are welcomed!

-jason

On Mon, 28 Apr 2003, Charles Hauser wrote:

> All,
>
> As far as I can tell all programs which return an HSP (blast, blat,
> sim4, exonerate) are all capable of informing you that a mismatch,gap or
> insert occurs in the HSP.
> However, none (as far as I can tell) inform you of the location of the
> mismatch, gap or insert.
>
> Specifically, I'm trying to proofread ESTs against genomic sequence as a
> quality step prior to assembling the ESTs into contigs and would like to
> mask any sequencing errors in the ESTs.
>
> Charles
>
>
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu