[Bioperl-l] Bio::Tools::BPbl2seq

[Peter Schattner]

Man-Suen Chan wrote:

> I have been using Bio::Tools::BPbl2seq to blast two sequences against each other where the query is a full length sequence and the subject is a shorter sequence which is repeated in the longer sequence. The bl2seq report shows several hits corresponding to these repeated regions. However the bioperl module appears to allow processing of the top hit only - (unless I have missed something).
> I would be grateful if anyone knows whether this is the case and whether there is any relatively easy way to parse the additional hits in these reports

If you e-mail me a copy of the script you are running and the bl2seq report you are parsing, I'll check how BPbl2seq is misbehaving.

Regards

Peter Schattner
schattner@alum.mit.edu