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<HTML>
<TITLE>Narrow PSSMs</title>
<H1 ALIGN=CENTER><IMG ALIGN=MIDDLE SRC="/blocks/icons/hutch_logo.gif">
Blocks WWW Server
<IMG ALIGN=MIDDLE SRC="/blocks/icons/blocks.xbm"></H1>
<P>
A service for biological sequence analysis at the
<A HREF="http://www.fhcrc.org/">Fred Hutchinson Cancer Research Center</A>
in Seattle, Washington, USA.
<HR>
<FORM ENCTYPE="MULTIPART/FORM-DATA" METHOD="POST" ACTION="/blocks-bin/narrow.pl">
<P>
This page will convert a narrow
<A HREF="help/narrow.block">block</A> ,
<A HREF="help/narrow.freq">frequency</A> or
<A HREF="help/narrow.weight">weight</A>
<A HREF="help/PSSM_def.html">PSSM</A> to
BLIMPS and
<A HREF="http://meme.sdsc.edu/meme/website/motif_format.html">MAST format</A>
and then search it vs
<A HREF="http://www.expasy.ch/sprot">Swiss-Prot</A> using
<A HREF="ftp://ftp.ncbi.nih.gov/repository/blocks/unix/blimps/">BLIMPS</A>.
<BR>
The conversion is done as follows:<BR>
<UL>
<LI>If a block is input, equal sequence weights are used.
<LI>If a block is input, amino acid frequencies are computed for each position.
<LI>If a block or frequency PSSM is input, minimal pseudo counts are
added to the actual counts; just enough to allow log-odds to be computed.
For a block, 1 pseudo-count per 10,000 real counts is computed using a substitution matrix.
For a frequency PSSM, 10,000 real counts and 1 pseudo-count are assumed
and the pseudo-count is computed using background frequencies.
<LI>If a block or frequency PSSM is input, the expected values for the
odds ratios are taken from Swiss-Prot and the log base e (scale in nats)
of the odds ratios is computed.
<LI>This PSSM is output in MAST format.
<LI>This PSSM is converted to a positive matrix and output in BLIMPS format.
<P>
If you have a multiple alignment, you can
<A HREF="process_blocks.html">reformat it</A>
as a
<A HREF="blocks_format.html">BLOCK</A>.
<P>
Select a query type:<BR>
<SELECT NAME="type" SIZE=3>
<OPTION VALUE="F" SELECTED> Frequency PSSM in MAST format
<OPTION VALUE="W"> Weight PSSM in MAST format
<OPTION VALUE="B"> Block
</SELECT>
<P>
Enter the name of a file containing your query:<BR>
<INPUT SIZE=50 NAME="qfile" TYPE="file"><BR>
-or-<BR>
Enter your query:<BR>
<TEXTAREA NAME="query" ROWS=10 COLS=60></TEXTAREA>
<HR>
<INPUT TYPE=submit>
<INPUT TYPE=reset>
<BR>
<HR>
<A href="contact.html">Contact us</A> <P>
Page last modified on <MODIFICATION_DATE>Mar 2003</MODIFICATION_DATE>
</HTML>
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