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

[Charles Hauser]

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