Hello, The file you mention:
chr1.phyloP46way.primate.wigFix actually contains phyloP scores, not phastCons scores. You can read more about both on the track description page here: http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=cons46way Note this section about negative phyloP scores: Another important difference is that phyloP can measure acceleration (faster evolution than expected under neutral drift) as well as conservation (slower than expected evolution). 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). The absolute values of the scores represent -log p-values under a null hypothesis of neutral evolution. The phastCons scores, by contrast, represent probabilities of negative selection and range between 0 and 1. Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 07/13/11 13:18, Randall, Thomas (NIH/NIEHS) [C] wrote: > Hi: > > > > I was trying to find the conserved regions in human 3'UTR and 5'UTR. I have > downloaded the multiple sequence alignment of primate. I was examining the > file, say, chr1.phyloP46way.primate.wigFix. It is my understanding that each > value corresponds to the probability of an nt being conserved at a given > position. That is, it must vary from 0 to 1 while 1 being highly conserved. > > > > But examining the file, it has negative value such as -2.34 etc... I am not > sure on how to interpret the phastCons value in the file.. > > > > I scanned through UCSC help or user's forum. Some others also have similar > questions, but no answer. Any help??? > > > > Thanks > Tom > > Thomas Randall, PhD > Bioinformatics Scientist, Contractor > National Institute of Environmental Health Sciences > P.O. Box 12233, Research Triangle Park, NC 27709 > [email protected]<mailto:[email protected]> > 919-541-2271 > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
