Good Afternoon Janeela: To confirm the measurements of phastCons and the question of alignment in any particular location, open up the alignment track displays and view the actual aligned bases to get a definite decision on the actual conservation for any particular location.
You may also find it useful to examine phastCons and phyloP conservation prediction tracks on the human Feb. 2009 (GRCh37/hg19) assembly in the 46-way conservation track. Please note the discussion of the meanings of phastCons and phyloP predictions: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&c=chr21&g=cons46way 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 genome at soe.ucsc.edu. --Hiram janeela khan wrote: > Dear all, > I am looking at the conservation of certain positions/regions using the > PhastConsElements28way, I got a score=0 and lod=132 for one of the position, > I am interested in knowing, what does this score means? I have read > http://compgen.bscb.cornell.edu/phast/phastCons-HOWTO.html to understand the > idea behind but it doesnot seems sufficeint. please guide me. > My interest is to see which of the positions are highly conserved in my data. > Thanks in advance, > Best janeela, _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
