Re: [EMBOSS] Help to build a motif for fzzpro
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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Re: [EMBOSS] Help to build a motif for fzzpro
Dear Aengus,
I have an idea of how to do it. You must of course complete the
motif/pattern as much as possible because with just {DE}(4) you will
find much to much unless you search only a few sequences. You must run
the program fuzzpro with parameter -rformat=listfile. You will obtain as
output an EMBOSS list file. You can then run fuzzpro again with as
sequence input list::xxx (xxx the name of your file) and as pattern
input @yyy where yyy contains :
basic_1
[HKR].
basic_2
x-[HKR].
basic_3
x-x-[HKR].
basic_4
x-x-x-[HKR].
Indeed, the input will contain only sequence fragments matching the
pattern and the basic amino acid hence should be in one of the first 4
positions.
Regards,
Guy Bottu,
ex-collaborator of the Belgian EMBnet Node
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Re: [EMBOSS] Help to build a motif for fzzpro
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
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