From beu99428 at ccsun50.iitd.ac.in  Sat May  1 14:50:01 2004
From: beu99428 at ccsun50.iitd.ac.in (E Ravikrishnan)
Date: Fri May  7 10:54:41 2004
Subject: [Jpred-list] Help needed in installing Jpred
Message-ID: <001001c42f55$19bda0c0$34018c0a@thegame>

Hi
I am final year student in IIT-Delhi. I need to run Jpred for secondary structure prediction for lot of proteins. 
I am kind of new..so
I need help in installing PSI-BLAST blast database for getting PSI-BLAST output.

thank you

Ravi
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From jon at compbio.dundee.ac.uk  Fri May  7 12:24:01 2004
From: jon at compbio.dundee.ac.uk (Jonathan Barber)
Date: Fri May  7 11:24:08 2004
Subject: [Jpred-list] Help needed in installing Jpred
In-Reply-To: <001001c42f55$19bda0c0$34018c0a@thegame>
References: <001001c42f55$19bda0c0$34018c0a@thegame>
Message-ID: <20040507102400.GC12662@flea.compbio.dundee.ac.uk>

On Sat, May 01, 2004 at 01:50:01PM +0530, E Ravikrishnan wrote:
> Hi
> I am final year student in IIT-Delhi. I need to run Jpred for
> secondary structure prediction for lot of proteins. 
> I am kind of new..so
> I need help in installing PSI-BLAST blast database for getting
> PSI-BLAST output.

The PSIBLAST database is formed by running the formatdb command on the
database download.

We use the SWISS-PROT (now Uniprot) FASTA download, and use the
following command line:
formatdb -o T -i swall.filt

However, we run programs to mask out low complexity regions of the
protein. We use seg (which is available with the NCBI blast download),
and helixfilt (from David Jones).

> thank you
> 
> Ravi
-- 
Jon