Hi,
The relevant papers describing the method in detail are:
PubMed:3656447
Gardiner-Garden M., Frommer M.
CpG islands in vertebrate genomes.
(20-Jul-1987) Journal of molecular biology, 196 (2) :261-82
PubMed:1505946
Larsen F., Gundersen G., Lopez R., Prydz H.
CpG islands as gene markers in the human genome.
(Aug-1992) Genomics, 13 (4) :1095-107
The source code - currently maintained by the EMBOSS team - is in the
EMBOSS distribution. See your <yourdir>/EMBOSS-5.0.0/emboss/newcpgreport.c
Hope this helps. Please do not hesitate to contact me if you have
further queries.
R:)
Staffa, Nick (NIH/NIEHS) wrote:
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
http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/newcpgreport.html
says:
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.
Thanks
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 ([EMAIL PROTECTED])
National Institute of Environmental Health Sciences
National Institutes of Health
Research Triangle Park, North Carolina
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