I have a set of 3'UTR mRNA sequence segment, I want to calculate the phastcons score of each nuleotide in the sequence. It is hard to extract the scores from UCSC conservation score files for i do not have the exact location of the sequence in the genome. So I wish to use the phastCons program the calculate the conservation score. In the phastCons HOWTO page http://compgen.cshl.edu/phast/phastCons-HOWTO.html it gives some example s such as phastCons [OPTIONS] alignment [cons.mod,]noncons.mod > scores.wig . But I don't know how to prepare these input files such as the alignment file. Does someone has ever calculated the PhastCons conservation score and tell me how to prepare the input files?
Need to obtain an answer ASAP,
All the best,