Comparative analysis and visualization of genomic sequences using VISTA browser and associated computational tools.

This chapter discusses VISTA Browser and associated computational tools for analysis and visual exploration of genomic alignments. The availability of massive amounts of genomic data produced by sequencing centers stimulated active development of computational tools for analyzing sequences and complete genomes, including tools for comparative analysis. Among algorithmic and computational challenges of such analysis, i.e., efficient and fast alignment, decoding of evolutionary history, the search for functional elements in genomes, and others, visualization of comparative results is of great importance. Only interactive viewing and manipulation of data allow for its in-depth investigation by biologists. We describe the rich capabilities of the interactive VISTA Browser with its extensions and modifications, and provide examples of the examination of alignments of DNA sequences and whole genomes, both eukaryotic and microbial. VISTA portal (http://genome.lbl.gov/vista) provides access to all these tools.