Hello Angus,
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])
Alternatively you could search with four different PROSITE-style patterns using fuzzpro and
combine the result tables:
[KRH]{DE}(3)
{DE}(1)[KRH]{DE}(2)
{DE}(2)[KRH]{DE}(1)
[KRH]{DE}(3)
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:
http://sapa-tool.uio.no/sapa/index.php
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.
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.
Best regards,
Josef
Josef Maier, IStLS Information Services to Life Science
> Date: Thu, 18 Oct 2012 15:52:44 +0100
> From: Aengus Stewart <aengus.stew...@cancer.org.uk>
> Subject: [EMBOSS] Help to build a motif for fzzpro
> To: emboss@lists.open-bio.org
> Message-ID: <508017bc.80...@cancer.org.uk>
> Content-Type: text/plain; charset="ISO-8859-1"; format=flowed
>
> Hi all,
>
> I have been asked to build a motif and the first part of the motif
> is.....
>
> "The first 4 AAs must not be acidic and 1 of them should be basic"
>
> I am not sure how to do this. So far I have
>
> {DE}(4)
>
> I am thinking I run with this and then post-filter the fuzzpro file?
>
>
> Any ideas greatfully accepted.
>
>
> Cheers
> Aengus
>
>
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