Accurate simulation and detection of coevolution signals in multiple sequence alignments.

ABSTRACT:

Background

While the conserved positions of a multiple sequence alignment (MSA) are clearly of interest, non-conserved positions can also be important because, for example, destabilizing effects at one position can be compensated by stabilizing effects at another position. Different methods have been developed to recognize the evolutionary relationship between amino acid sites, and to disentangle functional/structural dependencies from historical/phylogenetic ones.

Methodology/principal findings

We have used two complementary approaches to test the efficacy of these methods. In the first approach, we have used a new program, MSAvolve, for the in silico evolution of MSAs, which records a detailed history of all covarying positions, and builds a global coevolution matrix as th

SUBMITTER: Ackerman SH 

PROVIDER: S-EPMC3473043 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature