How to calculate phastcons scores for overlapping transcripts with different strands

Question

[biorepine]

Dear Biostars,

I am trying to calculate conservation scores for overlapping sense and anti-sense pairs of transcripts. Previously I used phastcons scores from ENCODE(mm9) to calculate conservation but irrespective of strand. Now I see that some times lncRNAs overlap protein-coding genes in an anti-sense manner. These lncRNAs are showing high levels of conservation because of its overlap. Therefore I am wondering is there any way to calculate conservation scores based on a strand ?

Thanx in advance

Answer 1

[Asaf]

Well, as far as I know, if a nucleotide is conserved its antisense is conserved as well, so no - conservation is in the DNA level and is obviously the same for both strands.

However, the conservation pattern of a protein coding gene will tend to have mutations on the 3rd nucleotides of the codons whereas non-coding RNAs have other conservation patternr, depending on their RNA families. Using these pattern you can sometimes distinguish between selective pressure that acted to conserve the protein sequence or to conserve the ncRNA sequence.