[BiO BB] BLAST problem: limiting # of HSPs
dmb at mrc-dunn.cam.ac.uk
Thu Mar 25 15:03:48 EST 2004
> 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
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
-b N (blastall, blastcl3, blastpgp, impala, megablast, rpsblast, seed-
Number of database sequences to show alignments for (B) (default
If you get an answer from blast-help at ncbi.nlm.nih.gov can you please post
it up? (these emails get archived).
> Kerr Wall
> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org
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