Comparative assessment of performance and genome dependence among phylogenetic profiling methods

Background: The rapidly increasing speed with which genome sequence data can be generated will be accompanied by an exponential increase in the number of sequenced eukaryotes. With the increasing number of sequenced eukaryotic genomes comes a need for bioinformatic techniques to aid in functional annotation. Ideally, genome context based techniques such as proximity, fusion, and phylogenetic profiling, which have been so successful in prokaryotes, could be utilized in eukaryotes. Here we explore the application of phylogenetic profiling, a method that exploits the evolutionary co-occurrence of genes in the assignment of functional linkages, to eukaryotic genomes. Results: In order to evaluate the performance of phylogenetic profiling in eukaryotes, we assessed the relative performance of commonly used profile construction techniques and genome compositions in predicting functional linkages in both prokaryotic and eukaryotic organisms. When predicting linkages in E. coli with a prokary...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Evan S. Snitkin, Adam M. Gustafson, Joseph C. Mellor, Jie Wu, Charles DeLisi
• Keywords: BMCBI 2006, Eukaryotic, Genomes, Profiles