Hello, According to the documentation for the PhyloP track data, the following is true:
> In the phyloP plots, sites predicted to be conserved are assigned > positive scores (and shown in blue), while sites predicted to be > fast-evolving are assigned negative scores (and shown in red). To view this information in context, please see the Methods section of the Conservation track. We hope this helps, Jennifer Jackson UCSC Genome Bioinformatics Group Anton Kratz wrote: > 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 > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
