Phylogenetic shadowing: sequence comparisons of multiple primate species

Abstract

Comparisons between the sequence of the human genome and that of species at a variety of evolutionary distances from human have emerged as one of the most powerful strategies for identifying the functional coding and non-coding elements in the genome. Although the analysis of traits shared between human and distant relatives such as mouse or chicken can be effectively carried out through comparisons among the genomes of those organisms, analysis of traits specific to primates requires comparisons with our closest non-human primate relatives. In addition, comparisons of highly similar sequences simplify many computational problems in comparative genomics. This chapter describes a strategy for sequence comparisons between multiple primate species.