Vista Family of Computational Tools for Comparative Analysis of Dna Sequences and Whole Genomes.
From: Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Methods in molecular biology (Clifton, N.J.)
- Publish Date: 2006
- ISSN: 1064-3745
- Volume: 338
- Issue:
- Pages: 69-89
- Medium: Print
- Language: English
- Citation (JAMA): Dubchak Inna, Ryaboy Dmitriy V, et al. Vista Family of Computational Tools for Comparative Analysis of Dna Sequences and Whole Genomes.. Methods Mol. Biol. 2006;338:69-89
Abstract
Comparative analysis of DNA sequences is becoming one of the major methods for discovery of functionally important genomic intervals. Presented here the VISTA family of computational tools was built to help researchers in this undertaking. These tools allow the researcher to align DNA sequences, quickly visualize conservation levels between them, identify highly conserved regions, and analyze sequences of interest through one of the following approaches: .Browse precomputed whole-genome alignments of vertebrates and other groups of organisms. .Submit sequences to Genome VISTA to align them to whole genomes. .Submit two or more sequences to mVISTA to align them with each other (a variety of alignment programs with several distinct capabilities are made available)..Submit sequences to Regulatory VISTA (rVISTA) to perform transcription factor binding site predictions based on conservation within sequence alignments.Use stand-alone alignment and visualization programs to run comparative sequence analysis locally All VISTA tools use standard algorithms for visualization and conservation analysis to make comparison of results from different programs more straightforward. The web page http://genome.lbl.gov/vista/ serves as a portal for access to all VISTA tools. Our support group can be reached by email at vista@lbl.gov.
Mesh Headings (Keywords): Algorithms, Animals, Computational Biology, Computer Graphics, Databases, Nucleic Acid, Genomics, Humans, Internet, Sequence Alignment, Sequence Analysis, DNA, Software
Check for Full Text / PubMed Unique Identifier (PMID): 16888351
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