Jerome,
What you are describing may be true (if so, its worth pursing), but my your
usage sounds very strange to me.
Having 7 fragments would be reasonable for a small cluster with 7
nodes. But for your GI filter file to only have 7 lines, would mean
that you would only be searching 7 sequences. When I search a
database such as NCBI's 'nt', my filterfile usually has more than
4,000,000 GIs.
The GI filter is used to include/exclude individual sequences when searching
your blastable database. This is done with the "-l filterfilename "(lowercase
L) command line switch, where filterfilename is (usually) a text file of GI #s,
one per line. Typically a blastable database will have thousands to millions of
sequences, and therefore thousands to millions of GIs.
The number of fragments refers to the number of pieces you split your blastable
database into. Commonly this will be the same size as the number of workers in
your cluster, or perhaps a multiple such as 2x or 3x larger.
In most cases the number of sequences in the database is many thousands of
times larger than the number of fragments. Otherwise each worker would have
very little work to do, and mpiBLAST probably wouldn't make much sense.
Does it sound like you and I are describing the same thing?
--
Mike Cariaso * Bioinformatics Software * http://www.cariaso.com
----- Original Message ----
From: Jerome <[EMAIL PROTECTED]>
To: [email protected]
Sent: Wednesday, March 14, 2007 7:55:28 PM
Subject: [Mpiblast-users] Strange issue in mpiBlast limiting by "Gi"
Hi all,
ive just instal a Mpiblast to running on our cluster. And it's a verya
fast program that i can thank's you!
For justa few day, some user want's to limit the search in a database of
bacterians genome. And i could notice that, if the number of "gi"
entries in the filter file is less or equivalent of the number of
fragments of the initial database, i don't matter about this filter file.
I mean that, for example, if i format the databases in 7 fragments, and
ask with a filter file size of >7 lines, i don't use it and answer the
similar response as if i don't use this filter.
Could someone help me in this issue?
--
-- Jérôme
Le vase donne une forme au vide, et la musique au silence.
(Georges Braque)
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