[Bioperl-l] BLAST problem: limiting # of HSPs

Kevin Beckmann kgb11 at psu.edu
Wed Mar 24 16:02:33 EST 2004

We've been using the Blast module of Bioperl to run tBLASTx locally against our
own data set.  We're looking for ways to reduce the output size produced by
BLAST and have set the alignment view to tabular(-m 8).  The problem that we've
come across is that a query will have multiple hits to the same sequence but
for different HSPs.  We need BLAST to retain only one result instead of filling
the BLAST report with multiple E values for HSPs from the same gene.  

In the default blast output, there are summary statistics for the overall hit,
is there an option for the tab-deliminated BLAST output that would give us this
overall hit statistic instead of one for each HSP?

If not, what is the option to limit the number of HSPs?

/ Kevin Beckmann \
\ kgb11 at psu.edu  /
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