Hello Ravid, Our wiki has some more information about the CpG islands track. Please see this page: http://genomewiki.cse.ucsc.edu/index.php/CpG_Islands
I hope this information is helpful to you. Please don't hesitate to contact us again if you require further assistance. Kayla Smith UCSC Genome Bioinformatics Group ravid straussman wrote: > Hi, > > The UCSC Genome browser CpG islands track has 28,226 islands. I've read the > description of the table but would still like to ask: > > Using the Gardiner-Garden criteria (%GC>50, CpG O/E > 0.6, length>200bp) one > would expect to find 307,193 islands in the human genome. Most of these are > indeed probably false negative results. > > The different thing that was done by your algorithm is the step were: "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." > > Can you explain the logic behind this criteria and how exactly is it > different from the classic criteria above? > > Many studies are now using the "NCBI-strict" definition of CpG islands where > the minimal length is set to 500bp in order to filter out the false-positive > results. Do you have any idea how these two alternatives compare? > > Is there some ref that explains more thoroughly the algorithm you were using? > > Thanks a lot, > > Ravid. > > > > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
