Unit

UNIT 10.6 Obtaining Comparative Genomic Data with the VISTA Family of Computational Tools

  1. Igor Ratnere,
  2. Inna Dubchak

Published Online: 1 JUN 2009

DOI: 10.1002/0471250953.bi1006s26

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Ratnere, I. and Dubchak, I. 2009. Obtaining Comparative Genomic Data with the VISTA Family of Computational Tools. Current Protocols in Bioinformatics. 26:10.6:10.6.1–10.6.17.

Author Information

  1. Lawrence Berkeley National Laboratory, Berkeley, California

Publication History

  1. Published Online: 1 JUN 2009
  2. Published Print: JUN 2009

Abstract

Comparison of DNA sequences from different species is a fundamental method for identifying functional elements, such as exons or enhancers, as they tend to exhibit significant sequence similarity due to purifying selection. Availability of whole-genome sequences for a constantly growing number of organisms makes identification of such elements within these genomes possible. There are two distinct phases in comparisons of genomic sequences: in the first, the sequences are aligned, and in the second, the resulting alignments are analyzed to find conservation signals that may be indicative of functional regions. Due to the considerable length of alignments, good visual representation techniques are a necessity for effective isolation of regions of interest. The VISTA family of tools provides biomedical investigators with a unified framework for the alignment of long genomic sequences and whole-genome assemblies, interactive visual analysis of alignments along with functional annotation, and many other comparative genomics capabilities. Curr. Protoc. Bioinform. 26:10.6.1-10.6.17. © 2009 by John Wiley & Sons, Inc.

Keywords:

  • comparative genomics;
  • DNA alignment;
  • VISTA;
  • genome browser