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<HTML>
<TITLE>Blocks Multiple Alignment Processor</TITLE>
<BODY>
<FORM ENCTYPE="MULTIPART/FORM-DATA" METHOD="POST" ACTION="/blocks-bin/process_blocks.pl">
<H1><IMG ALIGN=MIDDLE SRC="/blocks/icons/blocks.xbm">Blocks Multiple Alignment Processor</H1>
Blocks are carved out from a protein multiple sequence alignment to provide
input for:
<UL>
<LI>
<A HREF= "help/about_logos.html">Sequence logos</A>
<BR>
<LI>
<A HREF="help/about_trees.html">Phylogenetic trees</A>
<BR>
<LI>
<A HREF="http://www.proweb.org/3dblocks_intro.html">Structures</A>
<BR>
<LI>
<A HREF="/blocks/papers/BLOCKS_PERF.html">
Blocks-based searches</A>, which may be performed using search engines such as
<BR>
<UL>
<LI>
<A HREF="http://meme.sdsc.edu/meme/website/mast-intro.html">MAST</A>
<BR>
<LI>
<A HREF="help/LAMA_help.html">LAMA</A>
<BR>
</UL>
<LI>
<A HREF="help/CODEHOP/CODEHOP_help.html">CODEHOP</A> oligonucleotide primers
<BR>
<LI>
<A HREF="http://blocks.fhcrc.org/sift/SIFT.html">SIFT</A>
deleterious substitution predictions
</UL>
Your multiple alignment may include up to 400 sequences in one of
the following formats:
<UL>
<LI><A HREF="help/blocks_format.html">Blocks format</A>
such as is provided by
<A HREF="/blocks/make_blocks.html">Block Maker</A>.
<UL>
<LI>
You may <A HREF="block_formatter.html">format</A> alignments manually as blocks.
<P>
</UL>
<LI>
<A HREF="help/blocks_format.html#fasta">FASTA, CLUSTAL/STOCKHOLM or MSF format</A>.
<P>
</UL>
Ungapped regions between the requested minimum and maximum widths will be
carved out of the submitted multiple alignment and converted to Blocks format.
You can insert a column of gaps in your FASTA, CLUSTAL or MSF
alignment to force block edges.
<HR>
Enter the minimum block width:
<INPUT SIZE=3 NAME="minwidth" TYPE="text" VALUE="10"><BR>
Enter the maximum block width:
<INPUT SIZE=3 NAME="maxwidth" TYPE="text" VALUE="55"><BR>
Enter the name of a file containing your protein multiple alignment:<BR>
<INPUT SIZE=50 NAME="seqfile" TYPE="file"><BR>
-or-<BR>
Enter your protein multiple alignment below and <INPUT TYPE=submit VALUE=
"Submit">.<BR>
<TEXTAREA NAME="sequences" ROWS=10 COLS=60></TEXTAREA>
<HR>
<INPUT TYPE=submit VALUE="Submit">
<INPUT TYPE=reset VALUE="Clear Input">
<HR>
</FORM>
<P>
<A HREF="/blocks">[Blocks home]</A>
<A HREF="/blocks/blocks_search.html">[Block Searcher]</A>
<A HREF="/blocks/make_blocks.html">[Block Maker]</A>
<A HREF="/blocks-bin/getblock.sh">[Get Blocks]</A>
<A HREF="/blocks/block_formatter.html">[Blocks Formatter]</A>
<A HREF="/blocks-bin/LAMA_search.sh">[LAMA Searcher]</A>
<HR>
<A HREF="contact.html">Contact us</A> <P>
Page last modified <MODIFICATION_DATE>Aug 2003</MODIFICATION_DATE>
</BODY>
</HTML>
|
