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Title: Phylo-VISTA: Interactive visualization of multiple DNA sequence alignments

Abstract

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

Authors:
; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
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)
OSTI Identifier:
828738
Report Number(s):
LBNL-55265
R&D Project: LGFGAA; TRN: US200427%%664
DOE Contract Number:  
AC03-76SF00098
Resource Type:
Journal Article
Journal Name:
Bioinformatics
Additional Journal Information:
Journal Volume: 20; Journal Issue: 5; Other Information: Journal Publication Date: March 2004; PBD: 15 Jan 2004
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; ALGORITHMS; ALIGNMENT; AVAILABILITY; DATA ANALYSIS; DNA; INTERNET; JAVA; NAVIGATION

Citation Formats

Shah, Nameeta, Couronne, Olivier, Pennacchio, Len A, Brudno, Michael, Batzoglou, Serafim, Bethel, E Wes, Rubin, Edward M, Hamann, Bernd, and Dubchak, Inna. Phylo-VISTA: Interactive visualization of multiple DNA sequence alignments. United States: N. p., 2004. Web. doi:10.1093/bioinformatics/btg459.
Shah, Nameeta, Couronne, Olivier, Pennacchio, Len A, Brudno, Michael, Batzoglou, Serafim, Bethel, E Wes, Rubin, Edward M, Hamann, Bernd, & Dubchak, Inna. Phylo-VISTA: Interactive visualization of multiple DNA sequence alignments. United States. https://doi.org/10.1093/bioinformatics/btg459
Shah, Nameeta, Couronne, Olivier, Pennacchio, Len A, Brudno, Michael, Batzoglou, Serafim, Bethel, E Wes, Rubin, Edward M, Hamann, Bernd, and Dubchak, Inna. 2004. "Phylo-VISTA: Interactive visualization of multiple DNA sequence alignments". United States. https://doi.org/10.1093/bioinformatics/btg459.
@article{osti_828738,
title = {Phylo-VISTA: Interactive visualization of multiple DNA sequence alignments},
author = {Shah, Nameeta and Couronne, Olivier and Pennacchio, Len A and Brudno, Michael and Batzoglou, Serafim and Bethel, E Wes and Rubin, Edward M and Hamann, Bernd and Dubchak, Inna},
abstractNote = {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},
doi = {10.1093/bioinformatics/btg459},
url = {https://www.osti.gov/biblio/828738}, journal = {Bioinformatics},
number = 5,
volume = 20,
place = {United States},
year = {Thu Jan 15 00:00:00 EST 2004},
month = {Thu Jan 15 00:00:00 EST 2004}
}