[Bioperl-l] seq_word and pattern counts
Staffa, Nick (NIH/NIEHS) [C]
staffa at niehs.nih.gov
Tue Feb 28 21:46:30 UTC 2006
N matches any of the four bases.
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From: Torsten Seemann [mailto:torsten.seemann at infotech.monash.edu.au]
Sent: Tuesday, February 28, 2006 4:45 PM
To: Staffa, Nick (NIH/NIEHS) [C]
Cc: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] seq_word and pattern counts
> Does anyone know if Bio::Tools::SeqWords
> will do DNA pattern searches and honor ambiguity symbols
> like exist in some restriction enzyme pattern definitions,
> e.g. GGnnCC*
Examination of the code
suggests that all it does is count N-mers of any set of letters,
and does so in a case-insensitive way ie. CAT, Cat, cat are counted as
the same N-mer.
So no it does not handle ambiguity symbols in any special manner.
What would you like it to do?
If a N-mer has 1 "N" in it, does it count towards the 4 possible N-mers
it could be?
If it has 2 "N"s in it, does it count toward all 16 possible
And so on?
Victorian Bioinformatics Consortium, Monash University, Australia
Phone: +61 3 9905 9010
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