EShadow: a tool for comparing closely related sequences.

ABSTRACT: Primate sequence comparisons are difficult to interpret due to the high degree of sequence similarity shared between such closely related species. Recently, a novel method, phylogenetic shadowing, has been pioneered for predicting functional elements in the human genome through the analysis of multiple primate sequence alignments. We have expanded this theoretical approach to create a computational tool, eShadow, for the identification of elements under selective pressure in multiple sequence alignments of closely related genomes, such as in comparisons of human-to-primate or mouse-to-rat DNA. This tool integrates two different statistical methods and allows for the dynamic visualization of the resulting conservation profile. eShadow also includes a versatile optimization module capable of

SUBMITTER: Ovcharenko I 

PROVIDER: S-EPMC419798 | biostudies-literature | 2004 Jun

REPOSITORIES: biostudies-literature