[Bioperl-l] updating a reciprocal blast file
jason at bioperl.org
Thu Jun 5 16:18:40 EDT 2008
Are you keeping each pairwise in a separate file and then combining
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
> the directory of the the old proteomes in fasta format, and the pre-
> reciprocal blast file, and then performs the proper blasts and
> updates the
> pre-existing reciprocal blast file accordingly. I am using blast
> 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.
> View this message in context: http://www.nabble.com/updating-a-
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