  Genome-to-genome comparisons require designating anchor points, which are
given by Maximum Exact Matches (MEMs) between their sequences. For large
genomes this is a challenging problem and the performance of existing
solutions, even in parallel regimes, is not quite satisfactory. We present a
new algorithm, copMEM, that allows to sparsely sample both input genomes, with
sampling steps being coprime. Despite being a single-threaded implementation,
copMEM computes all MEMs of minimum length 100 between the human and mouse
genomes in less than 2 minutes, using less than 10 GB of RAM memory.
