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Bioinformatics Advance Access originally published online on January 22, 2004
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Bioinformatics 20(5) © Oxford University Press 2004; all rights reserved.

Phylo-VISTA: interactive visualization of multiple DNA sequence alignments

Nameeta Shah 1,*, Olivier Couronne 2,3, Len A. Pennacchio 2,3, Michael Brudno 5, Serafim Batzoglou 5, E. Wes Bethel 4, Edward M. Rubin 2,3, Bernd Hamann 1,4 and Inna Dubchak 2,3

1 Center for Image Processing and Integrated Computing, Department of Computer Science, One Shields Avenue, University of California, Davis, CA 95616-8562, USA, 2 US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA, 3 Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 4 Lawrence Berkeley National Laboratory, Berkeley, The University of California, CA 94720, USA and 5 Stanford University, Stanford, CA 94305, USA

Received on April 8, 2003 ; revised on October 1, 2003 ; accepted on October 2, 2003
Advance Access Publication January 22, 2004

Motivation: The power of multi-sequence comparison for biological discovery is well established. The need for new capabilities to visualize and compare cross-species alignment data is intensified by the growing number of genomic sequence datasets being generated for an ever-increasing number of organisms. To be efficient these visualization algorithms must support the ability to accommodate consistently a wide range of evolutionary distances in a comparison framework based upon phylogenetic relationships.

Results: We have developed Phylo-VISTA, an interactive tool for analyzing multiple alignments by visualizing a similarity measure for multiple DNA sequences. The complexity of visual presentation is effectively organized using a framework based upon interspecies phylogenetic relationships. The phylogenetic organization supports rapid, user-guided interspecies comparison. To aid in navigation through large sequence datasets, Phylo-VISTA leverages concepts from VISTA that provide a user with the ability to select and view data at varying resolutions. The combination of multiresolution data visualization and analysis, combined with the phylogenetic framework for interspecies comparison, produces a highly flexible and powerful tool for visual data analysis of multiple sequence alignments.

Availability: Phylo-VISTA is available at http://www-gsd.lbl.gov/phylovista. It requires an Internet browser with Java Plug-in 1.4.2 and it is integrated into the global alignment program LAGAN at http://lagan.stanford.edu

Contact: phylovista{at}lbl.gov

* To whom correspondence should be addressed.


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