Clustering of protein domains for functional and evolutionary studies.

ABSTRACT:

Background

The number of protein family members defined by DNA sequencing is usually much larger than those characterised experimentally. This paper describes a method to divide protein families into subtypes purely on sequence criteria. Comparison with experimental data allows an independent test of the quality of the clustering.

Results

An evolutionary split statistic is calculated for each column in a protein multiple sequence alignment; the statistic has a larger value when a column is better described by an evolutionary model that assumes clustering around two or more amino acids rather than a single amino acid. The user selects columns (typically the top ranked columns) to construct a motif. The motif is used to divide the family into subtypes using a stochastic optimi

SUBMITTER: Goldstein P 

PROVIDER: S-EPMC2770074 | biostudies-literature | 2009 Oct

REPOSITORIES: biostudies-literature