Hello Hannah, In general, if you are looking for a per-base measurement of conservation, the phyloP track is probably the most appropriate one. If the user wants to analyze a defined set of conserved regions, the phastCons elements are recommended. The phastCons wiggle is reflects how likely it is that a base is part of a conserved element, and takes into account neighboring bases.
For a more precise discussion of the differences between phyloP and phastCons you might want to consult the description page for the conservation track by clicking on the track name above the track pulldown or by clicking on the blue/gray bar to the left of the track in the main display. Hopefully this information was helpful and answers your question. If you have further questions or require clarification feel free to contact the mailing list at [email protected]. Regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu Hannah Watkins wrote: > Hello, > > I have been doing comparative analysis on the hg18 March 2006 > assembly. Sometimes there will be a high PhastCons score even though > the graphs that display the conservation of each animal individually > are very pale/non-existent and vice versa. Do you know if it is > better to focus on the density graphs or PhastCons score when trying > to get an idea of conservation in a particular region? Here is the > link for the session. > > > http://genome.ucsc.edu/cgi-bin/hgSession?hgsid=136701439&hgS_doSessionDetail=hg18_strong_graphs_no_phast > > Thanks, > Hannah > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
