Hello, We have developed a new Hidden Markov Model based method to look for CpG island (CGI) from DNA sequences. The existing definition of CGI (CG%>50%, O/E>0.6) was mainly derived from looking at promoters of known human genes. They might not work properly with newly discovered genomic marks (such as methylation regions) or other species with different nucleotide compositions. In our method the definition of CGI is totally data-driven, so that different species will have different cutoffs. Based on our experience the CGIs derived from our method have better overlaps with differentially methylated regions (DMRs) in human and mouse.
We currently have CGIs for following species: human (hg19 and hg18), mouse (mm9 and mm8), rat (rn4), chimp (panTro2), rhesus (rheMac2), orangutan (ponAbe2), cow (bosTau4), dog (canFam2), horse (equCab2), chicken (galGal3), zebrafish (danRer6), bee (apiMel2), fly (dm3), worm (ce2) and Arabidopsis. I’m wondering whether UCSC genome browser will be interested to add them as new tracks. If so please let me know how to proceed. Thank you very much. Best Regards, Hao Wu ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
