Dear UCSC-team, I have a list of a few thousand (putative) promoters in homo sapiens which I determined using my own computational method. The promoters are defined as a list of genomic start-end coordinates. I want to check whether these promoters are conserved in other species, using "phyloP44wayAll" from "Conservation - Vertebrate Multiz Alignment & Conservation".
However, phyloP44wayAll gives me scores at individual basepairs, what I need is a binary state conserved or non-conserved for each basepair (or region where the promoter is, does not need to be bp-resolution). I am aware that conservation is not necessarily a binary affair but I don't know how to check for it otherwise. So the goal is to convert the values from "phyloP44wayAll" conceptually into a series of conserved/non-conserved flags. Can you recommend a good approach to do this? I could select some arbitrary threshold but that would be rather unscientific. So I wonder how to determine a good threshold value, or if there is another possible approach to determine if my putative promoter regions are conserved or not? Thanks! Anton Kratz _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
