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Nucleic Acids Research 2004 32(Web Server Issue):W273-W279; doi:10.1093/nar/gkh458
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© 2004, the authors
Nucleic Acids Research, Vol. 32, Web Server issue © Oxford University Press 2004; all rights reserved

VISTA: computational tools for comparative genomics

Kelly A. Frazer, Lior Pachter1,2, Alexander Poliakov2, Edward M. Rubin2,3 and Inna Dubchak2,3,*

Perlegen Sciences, Inc., 2021 Stierlin Court, Mountain View, CA 94043, USA, 1 Department of Mathematics, University of California—Berkeley, Berkeley, CA, 94720, USA, 2 Genomics Division, Lawrence Berkeley National Laboratory, MS 84-171, Berkeley, CA 94720, USA and 3 Department of Energy Joint Genome Institute, 2800 Mitchell Avenue, Walnut Creek, CA 94598, USA

* To whom correspondence should be addressed. Tel: +1 510 495 2419; Fax: +1 510 486 5614; Email: ildubchak{at}lbl.gov

Received February 16, 2004; Revised and Accepted April 26, 2004

Comparison of DNA sequences from different species is a fundamental method for identifying functional elements in genomes. Here, we describe the VISTA family of tools created to assist biologists in carrying out this task. Our first VISTA server at http://www-gsd.lbl.gov/vista/ was launched in the summer of 2000 and was designed to align long genomic sequences and visualize these alignments with associated functional annotations. Currently the VISTA site includes multiple comparative genomics tools and provides users with rich capabilities to browse pre-computed whole-genome alignments of large vertebrate genomes and other groups of organisms with VISTA Browser, to submit their own sequences of interest to several VISTA servers for various types of comparative analysis and to obtain detailed comparative analysis results for a set of cardiovascular genes. We illustrate capabilities of the VISTA site by the analysis of a 180 kb interval on human chromosome 5 that encodes for the kinesin family member 3A (KIF3A) protein.

The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated.


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