Predicting protein linkages in bacteria: Which method is best depends on task

Background: Applications of computational methods for predicting protein functional linkages are increasing. In recent years, several bacteria-specific methods for predicting linkages have been developed. The four major genomic context methods are: Gene cluster, Gene neighbor, Rosetta Stone, and Phylogenetic profiles. These methods have been shown to be powerful tools and this paper provides guidelines for when each method is appropriate by exploring different features of each method and potential improvements offered by their combination. We also review many previous treatments of these prediction methods, use the latest available annotations, and offer a number of new observations. Results: Using Escherichia coli K12 and Bacillus subtilis, linkage predictions made by each of these methods were evaluated against three benchmarks: functional categories defined by COG and KEGG, known pathways listed in EcoCyc, and known operons listed in RegulonDB. Each evaluated method had strengths a...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Anis Karimpour-Fard, Sonia M. Leach, Ryan T. Gill, Lawrence Hunter
• Keywords: BMCBI 2008, Protein Functional Linkages, Proteins, Rosetta Stone