[BiO BB] BLAST problem: limiting # of HSPs

Kerr Wall pkerrwall at psu.edu
Thu Mar 25 13:51:38 EST 2004

We are runing 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, is there an option to limit the number of HSPs returned in the
tab-deliminated output?


Kerr Wall

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