Effect of reference genome selection on the performance of computational methods for genome-wide protein-protein interaction prediction.

ABSTRACT:

Background

Recent progress in computational methods for predicting physical and functional protein-protein interactions has provided new insights into the complexity of biological processes. Most of these methods assume that functionally interacting proteins are likely to have a shared evolutionary history. This history can be traced out for the protein pairs of a query genome by correlating different evolutionary aspects of their homologs in multiple genomes known as the reference genomes. These methods include phylogenetic profiling, gene neighborhood and co-occurrence of the orthologous protein coding genes in the same cluster or operon. These are collectively known as genomic context methods. On the other hand a method called mirrortree is based on the similarity of phylogeneti

SUBMITTER: Muley VY 

PROVIDER: S-EPMC3406042 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature