I have a set of genes from the Yeast genome (~3000) and a set of genes from Human genome (~6000). I want to align each yeast gene against each human gene, and get a similarity score for each pair. The lengths of the genes would be different, many pairs would be very dissimilar.
1) How would I go about doing this, say with R ? 2) Are there some specific things i should take into while doing my analysis?