Song G, Hsu CH, Riemer C, Miller W. Evaluation of methods for detecting conversion events in gene clusters.
BMC Bioinformatics 2011;
12 Suppl 1:S45. [PMID:
21342577 PMCID:
PMC3044302 DOI:
10.1186/1471-2105-12-s1-s45]
[Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND
Gene clusters are genetically important, but their analysis poses significant computational challenges. One of the major reasons for these difficulties is gene conversion among the duplicated regions of the cluster, which can obscure their true relationships. Many computational methods for detecting gene conversion events have been released, but their performance has not been assessed for wide deployment in evolutionary history studies due to a lack of accurate evaluation methods.
RESULTS
We designed a new method that simulates gene cluster evolution, including large-scale events of duplication, deletion, and conversion as well as small mutations. We used this simulation data to evaluate several different programs for detecting gene conversion events.
CONCLUSIONS
Our evaluation identifies strengths and weaknesses of several methods for detecting gene conversion, which can contribute to more accurate analysis of gene cluster evolution.
Collapse