[Genome] Conservation scores in an mRNA coordinate system

[Russell, Archie]

Hi,

I have some mRNA sequences for which I want the "conservation" scores
that are used in the Conservation wiggle track.   I want to conservation
scores for each base of the mRNA sequence, so it seems like this would
necessitate translating from genomic coordinates into mRNA coordinates.
Many of these mRNAs are not in the browser currently so they would
probably need to be aligned using BLAT as a first step.

What would be the best way to go about this?

Thanks,
Archie


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