newcpgreport vs newcpgseek

Rodrigo Lopez rls at
Sat Nov 16 01:08:02 UTC 2002

Hi Susan,

Yes. I never had the time to document these. Briefly:

newcpgreport use the same method to find islands but produce different
output. The method is described in:

Larsen,F., Gundersen,G., Lopez,R., Prydz,H. 
CpG islands as gene markers in the human genome. 
(1992) Genomics 13 (4):1095-107
MedlineID: 92372002     PubMedID: 1505946

Cpgreport uses a scoring method based on sum/frequencies which
overpredicts islands but finds the smaller ones around primary exons.

Cpgseek is deprecated at the moment.

For all practical purposes I use newcpgreport. I actually use it to
produce the human cpgisland database you can find on the EBI's ftp
server as well as on the EBI's SRS server.

Hope this helps,


> -----Original Message-----
> From: owner-emboss at 
> [mailto:owner-emboss at] On Behalf Of Susan J. Miller
> Sent: 15 November 2002 19:23
> To: emboss at
> Subject: newcpgreport vs newcpgseek
> I could not find an emboss there one?
> I'm trying to figure out the differences between cpgreport, 
> newcpgreport and newcpgseek.
> -- 
> Thanks,
> -susan
> Susan J. Miller
> Biotechnology Computing Facility
> Arizona Research Laboratories
> Bio West 228
> University of Arizona
> Tucson, AZ  85721
> (520) 626-2597

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