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<HTML>
<TITLE>Block Maker</TITLE>
<H1><IMG ALIGN=MIDDLE SRC="/blocks/icons/blocks.xbm"> Block Maker</H1>
<P>at the
<A HREF="http://www.fhcrc.org/">Fred Hutchinson Cancer Research Center</A>
BlockS WWW server.
<HR>
<FORM ENCTYPE="MULTIPART/FORM-DATA" METHOD="POST" ACTION="/blocks-bin/makeblocks.pl">
Block Maker finds conserved blocks in a group of
two or more <B>unaligned</B> protein sequences, which are assumed to be related,
using two different algorithms.<BR>
<B>If you already have a multiple alignment, please use the
<A HREF="/blocks/process_blocks.html">Multiple Alignment Processor</A>
instead.</B><P>
At least <STRONG>two</STRONG> related protein sequences must be provided
to make blocks.
Each sequence must have a unique name of <STRONG>10 characters or less</STRONG>.
If you have the accession numbers of some sequences you would like to use,
<A TARGET="entrez" HREF="http://www.ncbi.nlm.nih.gov/entrez/batchentrez.cgi?db=Nucleotide">Batch Entrez</A> can create a file for you in
<A HREF="http://www.ncbi.nlm.nih.gov/BLAST/fasta.html">FASTA format</A>.
<P>
If you have a file a sequences in a format other than FASTA, you can convert
them to FASTA format at the
<A HREF="http://www.ebi.ac.uk/cgi-bin/readseq.cgi">EBI conversion tool</A>.
<P>
It may take <STRONG>several minutes</STRONG> to
process your sequences. If you are not prepared to wait for a response,
or have more than 25 sequences or more than 15,000 amino acids,
please provide an email address and your
results will be returned to you in two messages. The second
message contains your blocks in
<A HREF="/blocks/blocks_format.html">Blocks Database format</A>,
and you can copy and paste these into the
<A HREF="/blocks/process_blocks.html">Multiple Alignment Processor</A>
to get
<A HREF="/blocks/help/about_logos.html">Logos</A> and
<A HREF="/blocks/help/about_trees.html">Trees</A>,
to search sequence database using
<A HREF="/blocks/help/about_cobbler.html">Cobbler</A>
or
<A HREF="http://meme.sdsc.edu/meme/website/mast-intro.html">Mast</A>,
and to predict PCR primers using <A HREF="/blocks/codehop.html">CODEHOPs</A>.
<HR>
Enter your email address if you want the results through email:<BR>
<INPUT SIZE=50 NAME="address"><P>
Enter a short description of your group of sequences:<BR>
<INPUT SIZE=20 NAME="desc"><P>
Enter the name of a file containing your protein sequences:<BR>
<INPUT SIZE=50 NAME="seqfile" TYPE="file"><BR>
-or-<BR>
Enter your protein sequences in a single format (e.g.
<A HREF="http://www.ncbi.nlm.nih.gov/BLAST/fasta.html">FASTA</A>):<BR>
<TEXTAREA NAME="sequences" ROWS=10 COLS=70></TEXTAREA>
<HR>
<INPUT TYPE=submit VALUE = "Make Blocks">
<INPUT TYPE=reset>
<P>
<STRONG>Note:</STRONG> It may take several minutes to compute the results:
Please be patient.
<HR>
You might be interested in trying other
<A HREF="http://dot.imgen.bcm.tmc.edu:9331/multi-align/multi-align.html">multiple sequence alignment methods</A>,
including ClustalW, MAP and PIMA, at the Human Genome Center at the Baylor
College of Medicine,
<A HREF="http://meme.sdsc.edu/meme/website/intro.html">Multiple EM for Motif Elicitation</A>
at the <A HREF="http://www.sdsc.edu/">San Diego Supercomputer Center</A>
and the
<A HREF="http://bayesweb.wadsworth.org/gibbs/gibbs.html">Gibbs Motif Sampler</A>
at the <A HREF="http://www.wadsworth.org">Wadsworth Center</A>.
<HR>
<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-bin/LAMA_search.sh">[LAMA Searcher]</A>
<HR>
<HR>
<A href="contact.html">Contact us</A> <P>
Page last modified on <MODIFICATION_DATE>Oct 2003</MODIFICATION_DATE>
</HTML>
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