[BiO BB] BLAST problem: limiting # of HSPs

[Dan Bolser]

> 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?


I think you can simply sum the e-values for each non overlapping HSP (I 
think they shouldn't overlap). Anybody know the correct formula?


> If not, is there an option to limit the number of HSPs returned in the
> tab-deliminated output?


I am sure there is a way to do this, but I can't find any mention of this
option in the 

ncbi/doc/blast.txt

file.

Hmm.... Not sure if these have anything to do with it...

-K N (blastall, blastcl3, blastpgp)
       Number  of  best  hits from a region to keep (off by default, if
       used a value of 100 is recommended)

-P N (blastall, blastpgp, rpsblast)
       Set to  1  for  single-hit  mode  or  0  for  multiple-hit
       mode (default)

-b N (blastall, blastcl3, blastpgp, impala, megablast, rpsblast, seed-
      top)
       Number of database sequences to show alignments for (B) (default
       is 250)

If you get an answer from blast-help at ncbi.nlm.nih.gov can you please post
it up? (these emails get archived).

Cheers,
Dan.

> 
> Thanks,
> 
> Kerr Wall
> 
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