It’s turned out to be a pretty good week. This one has been in press for ever, but finally hit the web:
Frith, M.C., Saunders, N.F.W., Kobe, B. and Bailey, T.L. (2008).
Discovering Sequence Motifs with Arbitrary Insertions and Deletions.
PLoS Computational Biology 4(4):e1000071. [Open Access] | [PubMed]
This paper describes GLAM2, a Gibbs sampler that finds and refines variable-width motifs, allowing insertion and deletion, in related but dissimilar sets of sequences. The work is Martin’s baby; my very minor contribution was to try it out on some test datasets. It’s open-access and open source, so you can all go and enjoy it then grab the software to try.
Two more (unrelated) in press to tell you about soon. See, I do have a day job outside of this blog.