A systematic study of genome context methods: calibration, normalization and combination

Background: Genome context methods have been introduced in the last decade as automatic methods to predict functional relatedness between genes in a target genome using the patterns of existence and relative locations of the homologs of those genes in a set of reference genomes. Much work has been done in the application of these methods to different bioinformatics tasks, but few papers present a systematic study of the methods and their combination necessary for their optimal use. Results: We present a thorough study of the four main families of genome context methods found in the literature: phylogenetic profile, gene fusion, gene cluster, and gene neighbor. We find that for most organisms the gene neighbor method outperforms the phylogenetic profile method by as much as 40% in sensitivity, being competitive with the gene cluster method at low sensitivities. Gene fusion is generally the worst performing of the four methods. A thorough exploration of the parameter space for each meth...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Luciana Ferrer, Joseph M. Dale, Peter D. Karp
• Keywords: BMCBI 2010, Business, Gene, Genome Context, Phylogenetic Profile