fuzznuc

[Gary Williams, Tel 01223 494522]

Philippe Dessen wrote:
> 
> Just a question about fuzznuc :
> Is it possible to define a pattern with repetition of a motif (as n
> letters with n>1) ?
> That is not mentionned in documentation .
> 
> The following pattern (a stop codon in a coding frame) seems to be
> illegal !
> <(NNN)(0,)TGA(NNN)(1,)>
> 
> $ fuzznuc seqfile
> Nucleic acid pattern search
> Search pattern: <(NNN)(0,)TGA(NNN)(1,)>
> Number of mismatches [0]:
> Output file [rptufrpx.fuzznuc]:
>    This is a warning: Illegal character [(]
> 
>    EMBOSS An error in fuzznuc.c at line 96:
> Illegal pattern


I think this is illegal in fuzznuc's PROSITE-style of pattern.
You might like to try 'dreg' instead with a regular expression like:

^(...)*TGA(...)+$

Note that these regilar expressions are case-sensitive, so put '-supper'
on your command  line to
force the sequence into the required upper case.

Gary

-- 
Gary Williams               Tel: +44 1223 494522  Fax: +44 1223 494512
mailto:G.Williams at hgmp.mrc.ac.uk            http://www.hgmp.mrc.ac.uk/
Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK