How to calcualte the phastCons score of a fake RNA sequence?

Question

[Bjoux]

There I have fake RNA seq which is shuffled from a real RNA seq, I want to obtain its phastcons score (conservation score). Apparently, I can not obtain it from UCSC phastcons files. Does someone has ever calculated the PhastCons conservation score and tell me how to get it?

Need to obtain an answer ASAP,

All the best,

Bjoux.

[Lars Juhl Jensen]

Considering that the phastCons score quantifies the conservation of something by comparing across genomes, it is difficult to see how one would even define - not to mention practically obtain - a phastCons score of something that is not in the genome. The question you are asking is basically this: how conserved is something that does not exist? If you have ended up in a situation where you need an answer to that question, I suspect you took a wrong turn somewhere earlier in your analysis.