Comparative study of the effectiveness and limitations of current methods for detecting sequence coevolution.

ABSTRACT:

Motivation

With rapid accumulation of sequence data on several species, extracting rational and systematic information from multiple sequence alignments (MSAs) is becoming increasingly important. Currently, there is a plethora of computational methods for investigating coupled evolutionary changes in pairs of positions along the amino acid sequence, and making inferences on structure and function. Yet, the significance of coevolution signals remains to be established. Also, a large number of false positives (FPs) arise from insufficient MSA size, phylogenetic background and indirect couplings.

Results

Here, a set of 16 pairs of non-interacting proteins is thoroughly examined to assess the effectiveness and limitations of different methods. The analysis shows that recent comp

SUBMITTER: Mao W 

PROVIDER: S-EPMC4481699 | biostudies-literature | 2015 Jun

REPOSITORIES: biostudies-literature