Frith MC, Noé L.

Nucleic Acids Res. 2014 Apr;42(7):e59. doi:10.1093/nar/gku104

Improved search heuristics find 20,000 new alignments between human and mouse genomes.

“using more codesigned seed patterns makes the alignment more sensitive but slower. The interesting point, though, is that using more seeds beats increasing the rareness threshold. For example, using four seeds with m 1⁄4 10 is both faster and more sensitive than one seed with m 1⁄4 100. The downside is that more seeds require more memory.” “We also tried aligning 10 000 random 1-kb chunks of the melanogaster genome to the pseudoobscura genome. In this case, the 1:1 [transitions:transversions] seeds perform better than the 3:2 seeds, as expected.” “Mammals have a greater excess than Drosophila, presumably because they have more methylcytosine, which mutates rapidly to thymine. Less-similar genomes have a lower excess of transitions: this is as expected because the transitions cannot keep increasing linearly but instead tend to an asymptote.”