GISMO

GISMO is a Markov chain Monte Carlo sampler for protein multiple sequence alignment. Features central to its performance are: (i) A “top-down” strategy with a favorable asymptotic time complexity that first identifies regions generally shared by all the sequences, and then realigns closely related subgroups in tandem. (ii) Inferred position-specific gap penalties that favor the placement of insertions between conserved blocks making up the proteins’ structural core. (iii)  A Bayesian statistical measure of alignment quality based on the minimum description length principle and on Dirichlet mixture priors. Consequently, GISMO aligns sequence regions only when statistically justified. This is unlike methods based on the ad hoc, but widely used, sum-of-the-pairs scoring system, which will align random sequences.