newcpgreport vs newcpgseek

[Rodrigo Lopez]

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,

R:)



> -----Original Message-----
> From: owner-emboss at hgmp.mrc.ac.uk 
> [mailto:owner-emboss at hgmp.mrc.ac.uk] On Behalf Of Susan J. Miller
> Sent: 15 November 2002 19:23
> To: emboss at embnet.org
> Subject: newcpgreport vs newcpgseek
> 
> 
> I could not find an emboss FAQ...is 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
>