title: Conversion events in gene clusters.
abstract: 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 (α-globin and β-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 http://www.bx.psu.edu/miller_lab.
  
  
  CONCLUSIONS
  These studies reveal the value of characterizing conversion events in the context of studying gene clusters in complex genomes.
authors.affiliation: Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16802 USA. gsong@bx.psu.edu
authors.forename: Giltae
authors.initials: G
authors.lastname: Song
authors.forename: Chih-Hao
authors.initials: CH
authors.lastname: Hsu
authors.forename: Cathy
authors.initials: C
authors.lastname: Riemer
authors.forename: Yu
authors.initials: Y
authors.lastname: Zhang
authors.forename: Hie Lim
authors.initials: HL
authors.lastname: Kim
authors.forename: Federico
authors.initials: F
authors.lastname: Hoffmann
authors.forename: Louxin
authors.initials: L
authors.lastname: Zhang
authors.forename: Ross C
authors.initials: RC
authors.lastname: Hardison
authors.forename: Eric D
authors.initials: ED
authors.lastname: Green
authors.forename: Webb
authors.initials: W
authors.lastname: Miller
mesh_terms: D000818:Animals; D019143:Evolution, Molecular; D005785:Gene Conversion; D016678:Genome; D006801:Humans; D008969:Molecular Sequence Data; D005810:Multigene Family; D010802:Phylogeny; D011323:Primates / Q000145:classification / Q000235:genetics*; D012984:Software; D055542:alpha-Globins / Q000235:genetics*; D055544:beta-Globins / Q000235:genetics*
chemical_list: D055542:alpha-Globins; D055544:beta-Globins