Hello Suganthi, The "overall score" field in the multiz table is not the PhastCons or PhyloP score; it is a field we use to display the multiz track as a single grayscale bar when it is in dense mode.
The PhastCons and PhyloP scores are downloadable here: http://hgdownload.cse.ucsc.edu/goldenPath/hg18/phastCons44way/ http://hgdownload.cse.ucsc.edu/goldenPath/hg18/phyloP44way/ Alternatively, see the scores in the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables), select the Conservation track, choose one of the phastCons44way* or phyloP44way* tables, enter a position range, and select "output format: data points". For a description of the phastCons data file format, see http://genome.ucsc.edu/goldenPath/help/phastCons.html (phyloP uses the same format). For a description of the differences between PhastCons and PhyloP scores, see the track description for the Conservation track. You can find the track description by clicking on the blue "Conservation" track name, by clicking on the gray mini-button to the left of the track, or by selecting the track in the Table Browser and hitting the "view table schema" button. If you have further questions, please feel free to contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 03/11/11 16:55, Suganthi Bala wrote: > Hi, > > I am trying to look for regions that are conserved in the human genome. I > see several options. I am trying to interpret the scores that come with each > option used. For eg, > I used the 44-species alignement and this is an example output > > 1347 chr10 100003294 100003484 28916644 8575806112 > 0.7316 > 1347 chr10 100003484 100003547 28916644 8575826654 > 0.727194 > 1347 chr10 100003547 100003576 28916644 8575836655 > 0.36254 > 1347 chr10 100003576 100003594 28916644 8575846077 > 0.439916 > 1347 chr10 100003594 100003625 28916644 8575853175 > 0.465818 > 1347 chr10 100003625 100003672 28916644 8575860760 > 0.487689 > > 1347 chr10 100003672 100003717 28916644 8575869528 > 0.513651 > > The last column is the overall score. CAn you give me a rough rule of > thumb as to how to interpret these scores. > I probably need to read about Phastcons and PhyloP to get a better > understanding of what the different conservation tracks are, but if > you can give me some idea about the 44-way alignment, > I will appreciate it. > > Many thanks. > > Best, > Suganthi > Yale University > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
