[EMBOSS] newcpgreport

Staffa, Nick (NIH/NIEHS) staffa at niehs.nih.gov
Thu Dec 20 21:44:02 UTC 2007

I have been using EMBOSS newcpgreport by
Rodrigo Lopez (rls © ebi.ac.uk)
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK

By default, this program defines a CpG island as a region where, over an
average of 10 windows, the calculated % composition is over 50% and the
calculated Obs/Exp ratio is over 0.6 and the conditions hold for a minimum
of 200 bases. These conditions can be modified by setting the values of the
appropriate parameters.

I may be very dull and unimaginative, but I'd sure like a more detailed
explanation of what the program is doing to define a CpG island.
Does anyone know where this might be found?
Or even the code.

Can anyone help please.

Nick Staffa 
Telephone: 919-316-4569  (NIEHS: 6-4569)
Scientific Computing Support Group
NIEHS Information Technology Support Services Contract
(Science Task Monitor: Roy W. Reter (reter at niehs.nih.gov)
National Institute of Environmental Health Sciences
National Institutes of Health
Research Triangle Park, North Carolina

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