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<div align="left"><font face="Arial" size="2"><span style=" font-size:10pt">Hello Angus,</span></font></div>
<div align="left"><font face="Arial" size="2"><span style=" font-size:10pt"><br />
</span></font></div>
<div align="left"><font face="Arial" size="2"><span style=" font-size:10pt">you could use preg with following pattern as written in regular expressions:
([KRH][^DE][^DE][^DE])|([^DE][KRH][^DE][^DE])|([^DE][^DE][KRH][^DE])|([^DE][^DE][^DE][KRH])</span></font></div>
<div align="left"><font face="Arial" size="2"><span style=" font-size:10pt"><br />
</span></font></div>
<div align="left"><font face="Arial" size="2"><span style=" font-size:10pt">Alternatively you could search with four different PROSITE-style patterns using fuzzpro and
combine the result tables:</span></font></div>
<div align="left"><font face="Arial" size="2"><span style=" font-size:10pt">[KRH]{DE}(3)</span></font></div>
<div align="left"><font face="Arial" size="2"><span style=" font-size:10pt">{DE}(1)[KRH]{DE}(2)</span></font></div>
<div align="left"><font face="Arial" size="2"><span style=" font-size:10pt">{DE}(2)[KRH]{DE}(1)</span></font></div>
<div align="left"><font face="Arial" size="2"><span style=" font-size:10pt">[KRH]{DE}(3)</span></font></div>
<div align="left"><font face="Arial" size="2"><span style=" font-size:10pt"><br />
</span></font></div>
<div align="left"><font face="Arial" size="2"><span style=" font-size:10pt">For searching with combinations of PROSITE patterns, amino acid compositions and
eventually AAINDEX profiles we had made a free web application for the University of Oslo,
the SAPA tool:</span></font></div>
<div align="left"><font face="Arial" size="2"><span style=" font-size:10pt">http://sapa-tool.uio.no/sapa/index.php</span></font></div>
<div align="left"><font face="Arial" size="2"><span style=" font-size:10pt"><br />
</span></font></div>
<div align="left"><font face="Arial" size="2"><span style=" font-size:10pt">E.g. searching a 4-letter subsequence with the PROSITE-style patterns "[KRH].{DE}(4)",
where the dot operator means logical AND, will produce a list of all subsequences having
the two patterns in that application.</span></font></div>
<div align="left"><font face="Arial" size="2"><span style=" font-size:10pt"><br />
</span></font></div>
<div align="left"><font face="Arial" size="2"><span style=" font-size:10pt">Maybe the possibility to combine more than one PROSITE-style pattern within a fuzzpro
search with logical AND would be a useful extension for fuzzpro improvement. Often more
than one pattern is given for a domain or functional site in the PROSITE pattern database.
Of course preg will do the job, however, the PROSITE patterns have to be rewritten as
regular expressions.</span></font></div>
<div align="left"><font face="Arial" size="2"><span style=" font-size:10pt"><br />
</span></font></div>
<div align="left"><font face="Arial" size="2"><span style=" font-size:10pt">Best regards,</span></font></div>
<div align="left"><font face="Arial" size="2"><span style=" font-size:10pt"><br />
</span></font></div>
<div align="left"><font face="Arial" size="2"><span style=" font-size:10pt">Josef</span></font></div>
<div align="left"><font face="Arial" size="2"><span style=" font-size:10pt"><br />
</span></font></div>
<div align="left"><font face="Arial" size="2"><span style=" font-size:10pt">Josef Maier, IStLS Information Services to Life Science</span></font></div>
<div align="left"><font face="Arial" size="2"><span style=" font-size:10pt"> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000" size="2"><span style=" font-size:10pt"><br />
</span></font></div>
<div align="left"><font face="Arial" color="#7f0000" size="2"><span style=" font-size:10pt">> Date: Thu, 18 Oct 2012 15:52:44 +0100</span></font></div>
<div align="left"><font face="Arial" color="#7f0000" size="2"><span style=" font-size:10pt">> From: Aengus Stewart <aengus.stewart@cancer.org.uk></span></font></div>
<div align="left"><font face="Arial" color="#7f0000" size="2"><span style=" font-size:10pt">> Subject: [EMBOSS] Help to build a motif for fzzpro</span></font></div>
<div align="left"><font face="Arial" color="#7f0000" size="2"><span style=" font-size:10pt">> To: emboss@lists.open-bio.org</span></font></div>
<div align="left"><font face="Arial" color="#7f0000" size="2"><span style=" font-size:10pt">> Message-ID: <508017BC.80002@cancer.org.uk></span></font></div>
<div align="left"><font face="Arial" color="#7f0000" size="2"><span style=" font-size:10pt">> Content-Type: text/plain; charset="ISO-8859-1"; format=flowed</span></font></div>
<div align="left"><font face="Arial" color="#7f0000" size="2"><span style=" font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000" size="2"><span style=" font-size:10pt">> Hi all,</span></font></div>
<div align="left"><font face="Arial" color="#7f0000" size="2"><span style=" font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000" size="2"><span style=" font-size:10pt">> I have been asked to build a motif and the first part of the motif</span></font></div>
<div align="left"><font face="Arial" color="#7f0000" size="2"><span style=" font-size:10pt">> is.....</span></font></div>
<div align="left"><font face="Arial" color="#7f0000" size="2"><span style=" font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000" size="2"><span style=" font-size:10pt">> "The first 4 AAs must not be acidic and 1 of them should be basic"</span></font></div>
<div align="left"><font face="Arial" color="#7f0000" size="2"><span style=" font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000" size="2"><span style=" font-size:10pt">> I am not sure how to do this. So far I have</span></font></div>
<div align="left"><font face="Arial" color="#7f0000" size="2"><span style=" font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000" size="2"><span style=" font-size:10pt">> {DE}(4)</span></font></div>
<div align="left"><font face="Arial" color="#7f0000" size="2"><span style=" font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000" size="2"><span style=" font-size:10pt">> I am thinking I run with this and then post-filter the fuzzpro file?</span></font></div>
<div align="left"><font face="Arial" color="#7f0000" size="2"><span style=" font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000" size="2"><span style=" font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000" size="2"><span style=" font-size:10pt">> Any ideas greatfully accepted.</span></font></div>
<div align="left"><font face="Arial" color="#7f0000" size="2"><span style=" font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000" size="2"><span style=" font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000" size="2"><span style=" font-size:10pt">> Cheers</span></font></div>
<div align="left"><font face="Arial" color="#7f0000" size="2"><span style=" font-size:10pt">> Aengus</span></font></div>
<div align="left"><font face="Arial" color="#7f0000" size="2"><span style=" font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000" size="2"><span style=" font-size:10pt">> </span></font></div>
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