Hello Li Jian,
These exact questions are answered in the Methods section of the track
description. To locate this, go into the assembly (hg18? hg19?), scroll
to the track group "Regulation" and click on the track name "CpG
Islands". Description, Credits, and References are also on this page.
-----quote------
CpG Islands
Methods
CpG islands were predicted by searching the sequence one base at a time,
scoring each dinucleotide (+17 for CG and -1 for others) and identifying
maximally scoring segments. Each segment was then evaluated for the
following criteria:
GC content of 50% or greater
length greater than 200 bp
ratio greater than 0.6 of observed number of CG dinucleotides to the
expected number on the basis of the number of Gs and Cs in the segment
The CpG count is the number of CG dinucleotides in the island. The
Percentage CpG is the ratio of CpG nucleotide bases (twice the CpG
count) to the length. The ratio of observed to expected CpG is
calculated according to the formula cited in Gardiner-Garden et al.
(1987) in the References section below:
Obs/Exp CpG = Number of CpG * N / (Number of C * Number of G)
where N = length of sequence.
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Thank you,
Jennifer
---------------------------------
Jennifer Jackson
UCSC Genome Informatics Group
http://genome.ucsc.edu/
On 5/4/10 1:20 PM, jian li wrote:
> Dear Sir or Madam,
> I have a quesiton about the defination of CpG island in UCSC. How do you
> define a CGI. That is GC content> ? %, ratio of the observed CpGs to the
> expected CpGs> ? , length> ? bp.
> Thank you very much for your help.
> Looking forward to getting your reply.
> Regards
> LI JIAN
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
