[Bioperl-l] finding sequence differences in BLAST output

[Paul Shinn]

   Hello,

   I'm trying to find a script that will report the location
and sequence of any sequence differences between the Query
and Subject sequences in a BLAST output.

   We're sequencing cDNA clones and we need to know the
location
and sequence of every sequence discrepancy between our clone
and the Arabidopsis genome.  I have a script that will go
through
a BLAST report of several sequences and tell me which
alignments
are 100% and which ones aren't, taking into account that
stretches
of "n"s are not discrepancies even though BLAST reports them
as
such.  Each of these discrepancies has to be annotated in
our
submission to Genbank.  A program to tell me the location
and
sequence would be much faster and accurate than counting
each base.

   Anyway, the script should report the location of
transversions/
transitions and insertions/deletions.  I'll try to figure it
out
on my own but I'm not the fastest coder.  Any help would be
appreciated.

					Thank you, Paul


-- 
Paul Shinn                   pshinn@neomorph.salk.edu
SIGnAL                       http://signal.salk.edu
Sequencing Coordinator       http://genome.salk.edu
(858) 453-4100 ext 1796