Hello Manisha, Yes, the positions are comparable, since all of the data (conservation track, ENSEMBL transcripts) are mapped using the same coordinate system to the reference genome.
But, there could be differences between the mRNA sequence and the reference genome sequence. The conservation track is based on reference genome sequence. You might need to consider doing some type of check to see if there are differences, where they are, and the differences matter for your project. Hopefully this helps, Jennifer On 3/5/10 9:24 AM, Manisha Brahmachary wrote: > Hello, > > > > I have used the ensemble 3'UTR sequences (hg19) downloaded from UCSC, to do a > motif search exercise. Now I want to use the conservation scores for > alignments of 45 vertebrate genomes with Human (hg 19) on these motif > positions to see which of the motif sites are more significant in terms of > evolutionary conservation. Since I have used ENSEMBL sequences, can I still > use these conservation scores ie. will the positions of the UTR sequences > differ from the one used to derive the conservation scores? > > > > Thanks > > > > Manisha Brahmachary, Ph.D. > > Associate Research Scientist > > 1130 St Nicholas Avenue > > ICRC,Room 802,Columbia University > > New York, NY 10032 > > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
