[EMBOSS] newcpgreport

Rodrigo Lopez rls at ebi.ac.uk
Fri Dec 21 09:11:05 UTC 2007


The relevant papers describing the method in detail are:

Gardiner-Garden M., Frommer M.
CpG islands in vertebrate genomes.
(20-Jul-1987) Journal of molecular biology, 196 (2) :261-82

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.


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 (reter at niehs.nih.gov)
> National Institute of Environmental Health Sciences
> National Institutes of Health
> Research Triangle Park, North Carolina

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