[Bioperl-l] limit the number of blast output per query

[Hans-Rudolf Hotz]

Hi

just double checking: are you really talking abut "10,000+ hits"? or do 
you mean "10,000+ HSPs" ('high-scoring segment pairs')?

I don't know how your genome database looks like, but assuming you have 
one sequence per chromosome, then you will get just 24 hits (ie each 
chromosome) and then depending on your query each hit will have a lot of 
HSPs.

As far as as I know, there is no way to limit the number of HSPs (you 
might try playing with the E value).

You can try using the tabular output format (this will reduce the file 
size) - or may be BLAST is not the right search tool for your task?


Regards, Hans


On 07/07/2011 04:43 AM, Ross KK Leung wrote:
> I know this question should submit to BLAST help but it seems they have
> already been overwhelmed by incoming emails. I wonder any bioperl users
> happen to know how to limit the number of blast output per query. For
> example, for human genome as a database to blast against, a single query can
> generate 10,000+ hits. I have already supplied -b 30 -v 30 flags but
> obviously the blastall from blast2.2.22 does not "obey" my instruction.
>
> The output files generated are usually larger than 100G+ but indeed the
> final ones that I want usually are only of 10M-. Is there any way to help
> save our Earth (Not exaggerated, energy is WASTED in a meaningless manner)?
>
>
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