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 _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
