Comparative analysis of DNA sequence from multiple species can provide insights 
into the function and evolutionary processes that shape genomes. The University 
of California Santa Cruz (UCSC) Genome Bioinformatics group has developed 
several tools and methodologies in its study of comparative genomics, many of 
which have been incorporated into the UCSC Genome Browser 
(http://genome.ucsc.edu), an easy-to-use online tool for browsing genomic data 
and aligned annotation "tracks" in a single window. The comparative genomics 
annotations in the browser include pairwise alignments, which aid in the 
identification of orthologous regions between species, and conservation tracks 
that show measures of evolutionary conservation among sets of multiply aligned 
species, highlighting regions of the genome that may be functionally important. 
A related tool, the UCSC Table Browser, provides a simple interface for 
querying, analyzing, and downloading the data underlying the Genome Browser 
annotation tracks. Here, we describe a procedure for examining a genomic region 
of interest in the Genome Browser, analyzing characteristics of the region, 
filtering the data, and downloading data sets for further study.