I have gene lists that I want to compare based on how well they were conserved across human and mice. Is there an established way of doing this? My first impulse was to compare identity directly but since genes have differing lengths and differing functional sizes of differing importance, a measure just based on sequence identity seems like a bad way of comparing any two genes to each other.
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Hi oganm, you can do this the complicated way or the easy way. The easy way is with identities (from Ensembl BioMart for instance) and the complicated way could be with a BLASTP similarity network.
Yes orthologs have differing length but in a pairwise comparison (like human-mouse), you have limited info.
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If you are interested in sequence conservation across species then you should look into 1) PhastCons scores (http://genome.ucsc.edu/goldenPath/help/phastCons.html, http://genome.cshlp.org/content/15/8/1034.long) or 2) GERP++ scores (http://mendel.stanford.edu/SidowLab/downloads/gerp/)