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

[Man-Suen Chan]

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
Thank you
Man-Suen Chan

Dr Man-Suen Chan
Department of Paediatrics
Institute of Molecular Medicine
University of Oxford
John Radcliffe Hospital
Oxford OX3 9DS, UK 
tel 01865 222310
tel 01865 287715 (Wellcome Trust Centre for Human Genetics)
fax 01865 222626
email: man-suen.chan@paediatrics.ox.ac.uk