H2r: identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments.

ABSTRACT:

Background

A multiple sequence alignment (MSA) generated for a protein can be used to characterise residues by means of a statistical analysis of single columns. In addition to the examination of individual positions, the investigation of co-variation of amino acid frequencies offers insights into function and evolution of the protein and residues.

Results

We introduce conn(k), a novel parameter for the characterisation of individual residues. For each residue k, conn(k) is the number of most extreme signals of co-evolution. These signals were deduced from a normalised mutual information (MI) value U(k, l) computed for all pairs of residues k, l. We demonstrate that conn(k) is a more robust indicator than an individual MI-value for the prediction of residues most plausibly i

SUBMITTER: Merkl R 

PROVIDER: S-EPMC2323388 | biostudies-literature | 2008 Mar

REPOSITORIES: biostudies-literature