Philippe Dessen dessen at infobiogen.fr
Mon Jul 16 12:25:38 UTC 2001

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 !

$ 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

in GCG syntax  you can use  (NNN){1,}


Philippe Dessen

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