Article: Pairwise alignment incorporating dipeptide covariation
G. E. Crooks, R. E. Brenner, S. E. Brenner, Bioinformatics 21:3704-3710 (2005)
Abstract
Standard algorithms for pairwise protein sequence alignment make the simplifying assumption that amino acid substitutions at neighboring sites are uncorrelated. This assumption allows implementation of fast algorithms for pairwise sequence alignment, but it ignores information that could conceivably increase the power of remote homolog detection.
