title: An effective method for detecting gene conversion events in whole genomes.
abstract: Gene conversion events are often overlooked in analyses of genome evolution. In a conversion event, an interval of DNA sequence (not necessarily containing a gene) overwrites a highly similar sequence. The event creates relationships among genomic intervals that can confound attempts to identify orthologs and to transfer functional annotation between genomes. Here we examine 1,616,329 paralogous pairs of mouse genomic intervals, and detect conversion events in about 7.5% of them. Properties of the putative gene conversions are analyzed, such as the lengths of the paralogous pairs and the spacing between their sources and targets. Our approach is illustrated using conversion events in primate CCL gene clusters. Source code for our program is included in the 3SEQ_2D package, which is freely available at www.bx.psu.edu/miller_lab/ .
authors.affiliation: Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16802, USA. cxh503@psu.edu
authors.forename: Chih-Hao
authors.initials: CH
authors.lastname: Hsu
authors.forename: Yu
authors.initials: Y
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: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D019143:Evolution, Molecular; D005785:Gene Conversion; D016678:Genome; D051379:Mice; D008969:Molecular Sequence Data; D005810:Multigene Family; D010802:Phylogeny; D011323:Primates / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*