[EMBOSS] Help to build a motif for fzzpro

[Peter Rice]

On 19/10/2012 10:33, Dr. Josef Maier - IStLS wrote:
> 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)

You can also put the four patterns in a file and use the syntax -pattern 
@patternfile

% cat patternfile
 >first
[KRH]{DE}(3)
 >second
{DE}(1)[KRH]{DE}(2)
 >third
{DE}(2)[KRH]{DE}(1)
 >fourth
[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

Interesting. I'll take a look.

> 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.

We also have a long standing offer to revive scrutineer, written by 
Peter Sibbald at EMBL some years ago but it would need translation from 
Pascal (not too hard to do). It loaded SwissProt into memory and had 
interesting ways to search for motif patterns.

regards,

Peter Rice
EMBOSS Team