Hello Hui Liu, I can't really tell you how to interpret the differences in conservation scores between homologous regions in the human, mouse and rat genomes, but perhaps I can point you to some helpful resources.
As you noticed, the conservation scores for each species are computed using a different set of aligned species, depending on what genomes are available at the time the track is constructed. Note also that there are actually two scores computed for human: conservation across all 28 species and an alternative measurement restricted to the placental mammal subset (17 species plus human) of the alignment. If you go to the details page for any of the Conservation tracks (click on the blue track name in the main Genome Browser display page, or on the blue or gray "mini-button" directly to the left of the track), you will see detailed information about how each track was constructed in the "Methods" section. You can also find several papers that may help you interpret the differences in conservation scores listed in the "References" section. Finally, you might want to look at the resources available on the PHAST website: http://compgen.bscb.cornell.edu/phast/index.php . I hope this is helpful. -- Brooke Rhead UCSC Genome Bioinformatics Group On 12/23/08 9:43 AM, Hui Liu wrote: > Hi all, > > I have a question about the conservation score comparing based on UCSC genome > browser data. > > I have notice that difference species use compute conservation score in > different ways. > For example human always compute conservation score with 28 species, mouse use > 30 and rat use 9. So if the conservation score of a base pair in human is > 0.3, the > conservation score of a base pair in mouse is 0.4 and a base pair in rat is > 0.5. Can I > say the 0.5 one is more conserved then the 0.3 and 0.4 one. > > Thanks > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
