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BMCBI
2010

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

8 years 5 months ago
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...
Luciana Ferrer, Joseph M. Dale, Peter D. Karp
Added 12 May 2011
Updated 12 May 2011
Type Journal
Year 2010
Where BMCBI
Authors Luciana Ferrer, Joseph M. Dale, Peter D. Karp
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