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Hello all,
I have a list of several thousand genomic positions for which I would like to get conservation scores (in the species Rattus norvegicus). By conservation scores I mean scores calculated by comparing multiple species sequence alignments, with methods such as PhastCons or SiPhy.
Does anyone have experience of doing this? I haven't found any conservation score data that is a very amendable format for doing this. PhastCons data that I have found (http://genome.ucsc.edu/goldenPath/help/phastCons.html) does not have the site associated with the score in a format I can readily use, it would require some non trivial processing. Some other scores I have found are not site specific but are for regions. I would much prefer site specific information.
If there is any preexisting software for this (perhaps designed for humans, in which case I could do liftOver of genomic coordinates) that might work too.
Any help or comments are greatly appreciated. Thanks in advance!
I have a list of several thousand genomic positions for which I would like to get conservation scores (in the species Rattus norvegicus). By conservation scores I mean scores calculated by comparing multiple species sequence alignments, with methods such as PhastCons or SiPhy.
Does anyone have experience of doing this? I haven't found any conservation score data that is a very amendable format for doing this. PhastCons data that I have found (http://genome.ucsc.edu/goldenPath/help/phastCons.html) does not have the site associated with the score in a format I can readily use, it would require some non trivial processing. Some other scores I have found are not site specific but are for regions. I would much prefer site specific information.
If there is any preexisting software for this (perhaps designed for humans, in which case I could do liftOver of genomic coordinates) that might work too.
Any help or comments are greatly appreciated. Thanks in advance!