Hello, You are correct, the positive values are for conserved regions:
> 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. There is no specific recommended threshold for "highly conserved", but the author of the tool does have some suggestions for determining your own in another prior response: https://lists.soe.ucsc.edu/pipermail/genome/2005-October/008744.html We hope this helps, ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Chirag Nepal" <[email protected]> wrote: > From: "Chirag Nepal" <[email protected]> > To: [email protected] > Sent: Thursday, September 24, 2009 5:41:02 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] Genome Multiple alignment score > > Dear UCSC, > > In addition to the reply from previous post. > > > ################ > Hello again, Wen, > > We just display the data and allow you to draw your own conclusions > about > significance. That said, the MAF scores are not a good measure of > conservation > -- you might consider looking instead at additional analysis methods > to > determine this. > > For example, you could view the "Most Conserved" track in the genome > browser. > This track shows predictions of conserved elements produced by the > phastCons > program based on a whole-genome alignment of vertebrates, and for the > > placental > mammal subset of species in the alignment. They are based on a > phylogenetic > hidden Markov model (phylo-HMM), a type of probabilistic model that > describes > both the process of DNA substitution at each site in a genome and the > way this > process changes from one site to the next. > > I hope this information is helpful to you. Please don't hesitate to > contact > the mail list again if you require further assistance. > > ################### > > > I would like to know if there is any measure ot threshold score, which > > can give us a rough idea about how well the sequence is conserved. > When we look at the score, some have -ve value, while some have +ve > and 0 value. > > Does all -ve score means they r not very conserved (by eye it looks > like they r not conserved). > BUt for +ve score, is there any sort of threshold which determines > > whether the sequence in the alignmnet is highly conserved or not. > > > regards > Chirag > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
