[BioC] PWMscoreStartingAt and ambiguous subject seqs

Janet Young jayoung at fhcrc.org
Tue May 22 03:34:11 CEST 2012

Hi there,

I'm using PWMscoreStartingAt from Biostrings - it's VERY useful for me - thanks!

Some of the sequences I'm scanning include ambiguities (some N, some Y, etc - uses IUPAC codes).  I'm really glad that PWMscoreStartingAt works on these sequences, but I'd like to understand how scores are calculated when an N (or whatever) is present - would it be easy for you to add that to the documentation?  (or just an email response would be fine too, but seems useful to add it to the docs)

thanks very much,



Dr. Janet Young 

Tapscott and Malik labs

Fred Hutchinson Cancer Research Center
1100 Fairview Avenue N., C3-168, 
P.O. Box 19024, Seattle, WA 98109-1024, USA.

tel: (206) 667 1471 fax: (206) 667 6524
email: jayoung  ...at...  fhcrc.org


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