newcpgreport vs newcpgseek
rls at ebi.ac.uk
Sat Nov 16 01:08:02 UTC 2002
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 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.
> 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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