Hi Rad, Changing the species selected for display in the Conservation track has no effect on the phastCons or phyloP scores. The scores are calculated once, when we create the track. Note, however, that there are 3 different sets of phastCons scores: one for all 44 species (referred to as "vertebrate conservation"), one for only the placental mammals, and one for only the primates.
The phastCons scores that are available on the mouse browser are a separate calculation. On the mm9 browser, there is a 30-way Conservation track, and there are phastCons scores for 3 different sets: all 30 species, mammals only, and euarchontoglires only. phastCons scores for either the human or the mouse tracks can be obtained from the Table Browser by selecting the Conservation track, then the phastConsXXway (or phastConsXXwayPlacental, etc.) table, and output format: data points. If you have a set of regions, you can hit the "defined regions" button to limit the output to only those regions. Alternatively, you can download the entire phastCons dataset from (for human): http://hgdownload.cse.ucsc.edu/goldenPath/hg19/phastCons46way/ and for mouse: http://hgdownload.cse.ucsc.edu/goldenPath/mm9/phastCons30way/ I hope this answers your questions. If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 7/12/12 10:37 AM, Mohamed Radhouane Aniba wrote: > Hello everyone, > > I played a lot with conservation tracks on UCSC genome browser and I > know that we can select species and deselect some others. Now this > conservation if I understood well, are pre-calculated for let's say > 44 species. If we select only human and mouse for display, is the > plot shown in the browser corresponding to phastCons score ONLY for > Human and Mouse or are these score for the 44 species and only Human > and Mouse are shown. > > If it is the case, I have some regions in Human that I want to map to > corresponding region in Mouse to extract phastCons scores, is there a > way of doing it using the browser or UCSC Tables ? Any MySQL query is > welcome as well. > > Regards, > > Rad > > Radhouane Aniba Bioinformatics Postdoctoral Research Scientist > Institute for Advanced Computer Studies Center for Bioinformatics and > Computational Biology (CBCB) University of Maryland, College Park MD > 20742 > > _______________________________________________ Genome maillist - > [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
