[Bioperl-l] Repeat element check

[Brian Osborne]

Govind,

The "III.4.1 Running BLAST (using RemoteBlast.pm)" section in bptutorial.pl
talks about this in a general way, but doesn't address your questions
specifically. I've never done this but I'd guess you'd set the human repeat
masker like this:

$Bio::Tools::Run::RemoteBlast::HEADER{'FILTER'} = 'R';

See http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html.

However I don't see how you set low complexity filter = off and human repeat
masking = on at the same time using Bioperl since they're both FILTER
parameters. I'd be interested in seeing your solution, should you find one.

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of M K. Govind
Sent: Thursday, May 22, 2003 5:57 AM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] Repeat element check

Hi all

I have been using the Bioperl TOOls module (Remote blast) for
submitting blast request to NCBI.

I belive that the low complexity filter is on when blast is
submitted to the NCBI using this module.
I would like to know

1..How do i turn the low complexity filter off
2. How do i use the human repeat masker . (The NCBI blast web site
has got a parameter in blast page )
3.Is there anyway that we could use the human repeat masker along
with the remote blast?

Thanks in advance
-Govind
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