Protein sequence alignment analysis by local covariation: coevolution statistics detect benchmark alignment errors.

ABSTRACT: The use of sequence alignments to understand protein families is ubiquitous in molecular biology. High quality alignments are difficult to build and protein alignment remains one of the largest open problems in computational biology. Misalignments can lead to inferential errors about protein structure, folding, function, phylogeny, and residue importance. Identifying alignment errors is difficult because alignments are built and validated on the same primary criteria: sequence conservation. Local covariation identifies systematic misalignments and is independent of conservation. We demonstrate an alignment curation tool, LoCo, that integrates local covariation scores with the Jalview alignment editor. Using LoCo, we illustrate how local covariation is capable of identifying alignment error

SUBMITTER: Dickson RJ 

PROVIDER: S-EPMC3371027 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature