Phylo-VISTA: Interactive visualization of multiple DNA sequence alignments
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 Plugin 1.4.2 and it is integrated into the global alignment program LAGAN at http://lagan.stanford.edu
- Research Organization:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Organization:
- USDOE. Laboratory Directed Research and Development; National Science Foundation Contract ACI 9624034, National Science Foundation Graduate Fellowship, National Heart Lung and Blood Institute. Program for Genomic Applications grant, National Partnership for Advanced Computational Infrastructure; Large Scientific and Software Data Set Visualization Program Contract ACI 9982251 (US)
- DOE Contract Number:
- AC03-76SF00098
- OSTI ID:
- 828738
- Report Number(s):
- LBNL-55265; R&D Project: LGFGAA; TRN: US200427%%664
- Journal Information:
- Bioinformatics, Vol. 20, Issue 5; Other Information: Journal Publication Date: March 2004; PBD: 15 Jan 2004
- Country of Publication:
- United States
- Language:
- English
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Phylo-VISTA: An interactive visualization tool for multiple DNAsequence alignments
Phylo-VISTA: An Interactive Visualization Tool for Multiple DNA Sequence Alignments