1b17e173bde7713fe7080825f27efb8e952419f4 hiram Thu Aug 1 14:51:39 2019 -0700 updating text after QA comments refs #23734 diff --git src/hg/utils/automation/asmHubCpG.pl src/hg/utils/automation/asmHubCpG.pl index 530a6de..d3b943e 100755 --- src/hg/utils/automation/asmHubCpG.pl +++ src/hg/utils/automation/asmHubCpG.pl @@ -53,36 +53,30 @@ DNA strand from the parent strand, which aids in the final stages of DNA proofreading after duplication. However, over evolutionary time, methylated Cs tend to turn into Ts because of spontaneous deamination. The result is that CpGs are relatively rare unless there is selective pressure to keep them or a region is not methylated for some other reason, perhaps having to do with the regulation of gene expression. CpG islands are regions where CpGs are present at significantly higher levels than is typical for the genome as a whole.</p> <p> The unmasked version of the track displays potential CpG islands that exist in repeat regions and would otherwise not be visible in the repeat masked version. </p> -<p> -By default, only the masked version of the track is displayed. To view the -unmasked version, change the visibility settings in the track controls at -the top of this page. -</p> - <h2>Methods</h2> <p>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: <ul> <li>GC content of 50% or greater</li> <li>length greater than 200 bp</li> <li>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</li> </ul> </p> <p>