[Bioperl-l] updating a reciprocal blast file

Jason Stajich jason at bioperl.org
Thu Jun 5 16:18:40 EDT 2008

Are you keeping each pairwise in a separate file and then combining  
it all?

Are you fixing E-values so they are scaled across different sized  
databases? You will probably want to add a Z= parameter to insure  
values are useable.

I also had to hack ORTHOMCL locally to cache things in DB_Files as it  
was too memory intensive the way it runs on my big datasets.

On Jun 5, 2008, at 8:53 AM, JustinV wrote:

> I have a large reciprocal blast file that contains 3 proteomes.   
> I'd like to
> integrate another proteome for downstream clustering.    I imagine a
> command-line script that takes as input the new proteome in fasta  
> format,
> the directory of the the old proteomes in fasta format, and the pre- 
> existing
> reciprocal blast file, and then performs the proper blasts and  
> updates the
> pre-existing reciprocal blast file accordingly.  I am using blast  
> locally
> and the downstream processing is done by OrthoMCL.  I assume this  
> has been
> handled before, but I can't track down the code.  If anyone is  
> familiar with
> a pre-exisiting script or has pertinent advice, I'd be much obliged.
> Justin
> -- 
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