How Do I Get A Phylop Input File?

Question

[Stephanhart]

I would like to find conservation scores between a limited number of primate species for a protein-coding gene. As I understand it, the phyloP input file looks like this:

chr22  16440426  14440427  C/T

Starting with an Ensembl ID for my gene, how can I generate this type of file. Any help is appreciated.

Thanks
Stephan

Answer 1

[spacemorrissey]

I am not completely clear on what you want, but if you are looking for the conservation score across a gene or a group of genes, you can simply look up the location of the gene. Once you have the chrom, start, and stop in bed format, you can download the PhyloP bigwig track from the UCSC browser and use BigwigAverageOverBed to get the score across the gene, or list of genes.