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Phylo-VISTA: interactive visualization of multiple DNA sequence alignments.

Nameeta Shah·Olivier Couronne·Len A Pennacchio·Michael Brudno·Serafim Batzoglou·E Wes Bethel·Edward M Rubin·Bernd Hamann·Inna Dubchak
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Abstract

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

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AlgorithmsAnimalsBase SequenceComputer GraphicsGene Expression ProfilingHumansLeukemiaMolecular Sequence DataPhylogenySequence AlignmentSequence Analysis, DNASequence Homology, Nucleic AcidSoftwareUser-Computer InterfaceComparative StudyEvaluation StudyJournal ArticleResearch Support, Non-U.S. Gov'tResearch Support, U.S. Gov't, Non-P.H.S.Research Support, U.S. Gov't, P.H.S.Validation Study

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Nameeta Shah, Olivier Couronne, Len A Pennacchio, Michael Brudno, Serafim Batzoglou, E Wes Bethel, Edward M Rubin, Bernd Hamann, Inna Dubchak. 2004-01-22. Phylo-VISTA: interactive visualization of multiple DNA sequence alignments.. https://doi.org/10.1093/bioinformatics%2Fbtg459

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