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+[[!meta title="Improved search heuristics find 20,000 new alignments between human and mouse genomes."]]
+[[!tag LAST alignment]]
+
+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.
+
+[[!pmid 24493737 desc="“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.”"]]

diff --git a/tags/LAST.mdwn b/tags/LAST.mdwn
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 _bibliography in progress..._
 
+ - `lastdb` can use various seeding schemes to build its index.
+    [[Frith and Noé (2014)|biblio/24493737]] discuss some of them.
+
  - `last-postmask` ([[Frith, 2011|biblio/22205972]]): discards alignments that
    contain a significant amount of lower-case-masked sequences.