title: Comparative genomics approaches to study organism similarities and differences.
abstract: Comparative genomics is a large-scale, holistic approach that compares two or more genomes to discover the similarities and differences between the genomes and to study the biology of the individual genomes. Comparative studies can be performed at different levels of the genomes to obtain multiple perspectives about the organisms. We discuss in detail the type of analyses that offer significant biological insights in the comparisons of (1) genome structure including overall genome statistics, repeats, genome rearrangement at both DNA and gene level, synteny, and breakpoints; (2) coding regions including gene content, protein content, orthologs, and paralogs; and (3) noncoding regions including the prediction of regulatory elements. We also briefly review the currently available computational tools in comparative genomics such as algorithms for genome-scale sequence alignment, gene identification, and nonhomology-based function prediction.
authors.affiliation: Nexus Genomics, Inc., 229 Polaris Ave., Suite 6, Mountain View, CA 94043, USA. wei@nexusgenomics.com
authors.forename: Liping
authors.initials: L
authors.lastname: Wei
authors.forename: Yueyi
authors.initials: Y
authors.lastname: Liu
authors.forename: Inna
authors.initials: I
authors.lastname: Dubchak
authors.forename: John
authors.initials: J
authors.lastname: Shon
authors.forename: John
authors.initials: J
authors.lastname: Park
mesh_terms: D000818:Animals; D001482:Base Composition / Q000235:genetics; D005796:Genes / Q000235:genetics; D023281:Genomics / Q000379:methods*; D006801:Humans; D013045:Species Specificity