To whom it may concern:
I am interested in obtaining the program that was used in generating the CpG
Islands for the zebrafish genome found on UCSC genome browser, or more
information pertaining to the first section of identifying maximally coring
segment. Is this program publically available or could I get in touch with the
person who ran this program?
Thank You,
Magdalena Potok ( graduate student in Brad Cairns Lab at the University of
Utah).
Below is the description form UCSC on the CpG island track:
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)):
Obs/Exp CpG = Number of CpG * N / (Number of C * Number of G)
where N = length of sequence.
Credits
This track was generated using a modification of a program developed by G.
Miklem and L. Hillier (unpublished).
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