Conversion events in gene clusters

Giltae Song, Chih Hao Hsu, Cathy Riemer, Yu Zhang, Hie Kim, Federico Hoffmann, Louxin Zhang, Ross C. Hardison, Eric D. Green, Webb Miller

Research output: Contribution to journalArticlepeer-review

11 Scopus citations


Background: Gene clusters containing multiple similar genomic regions in close proximity are of great interest for biomedical studies because of their associations with inherited diseases. However, such regions are difficult to analyze due to their structural complexity and their complicated evolutionary histories, reflecting a variety of large-scale mutational events. In particular, conversion events can mislead inferences about the relationships among these regions, as traced by traditional methods such as construction of phylogenetic trees or multi-species alignments. Results: To correct the distorted information generated by such methods, we have developed an automated pipeline called CHAP (Cluster History Analysis Package) for detecting conversion events. We used this pipeline to analyze the conversion events that affected two well-studied gene clusters (-globin and -globin) and three gene clusters for which comparative sequence data were generated from seven primate species: CCL (chemokine ligand), IFN (interferon), and CYP2abf (part of cytochrome P450 family 2). CHAP is freely available at Conclusions: These studies reveal the value of characterizing conversion events in the context of studying gene clusters in complex genomes.

Original languageEnglish (US)
Article number226
JournalBMC Evolutionary Biology
Issue number1
StatePublished - 2011

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics


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