Integration of phenotypic metadata and protein similarity in Archaea using a spectral bipartitioning approach.

ABSTRACT: In order to simplify and meaningfully categorize large sets of protein sequence data, it is commonplace to cluster proteins based on the similarity of those sequences. However, it quickly becomes clear that the sequence flexibility allowed a given protein varies significantly among different protein families. The degree to which sequences are conserved not only differs for each protein family, but also is affected by the phylogenetic divergence of the source organisms. Clustering techniques that use similarity thresholds for protein families do not always allow for these variations and thus cannot be confidently used for applications such as automated annotation and phylogenetic profiling. In this work, we applied a spectral bipartitioning technique to all proteins from 53 archaeal genomes

SUBMITTER: Hooper SD 

PROVIDER: S-EPMC2673424 | biostudies-literature | 2009 Apr

REPOSITORIES: biostudies-literature