Identification of divergent protein domains by combining HMM-HMM comparisons and co-occurrence detection.

ABSTRACT: Identification of protein domains is a key step for understanding protein function. Hidden Markov Models (HMMs) have proved to be a powerful tool for this task. The Pfam database notably provides a large collection of HMMs which are widely used for the annotation of proteins in sequenced organisms. This is done via sequence/HMM comparisons. However, this approach may lack sensitivity when searching for domains in divergent species. Recently, methods for HMM/HMM comparisons have been proposed and proved to be more sensitive than sequence/HMM approaches in certain cases. However, these approaches are usually not used for protein domain discovery at a genome scale, and the benefit that could be expected from their utilization for this problem has not been investigated. Using proteins of P. fa

SUBMITTER: Ghouila A 

PROVIDER: S-EPMC4046975 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature