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Related Experiment Videos

VISTA: computational tools for comparative genomics.

Kelly A Frazer1, Lior Pachter, Alexander Poliakov

  • 1Perlegen Sciences, Inc., 2021 Stierlin Court, Mountain View, CA 94043, USA.

Nucleic Acids Research
|June 25, 2004
PubMed
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The VISTA tools facilitate comparative genomics by aligning and visualizing DNA sequences to identify functional elements. This aids biologists in genome analysis and understanding gene function across species.

Area of Science:

  • Genomics
  • Bioinformatics
  • Comparative Genomics

Background:

  • Comparing DNA sequences across species is crucial for identifying functional genomic elements.
  • The VISTA family of tools was developed to aid biologists in this comparative genomics task.
  • The initial VISTA server was launched in 2000 for aligning and visualizing genomic sequences.

Purpose of the Study:

  • To describe the VISTA family of tools for comparative genomic analysis.
  • To highlight the capabilities of the VISTA site for browsing alignments and performing custom analyses.
  • To demonstrate the utility of VISTA through the analysis of a specific human genomic region.

Main Methods:

  • Utilizing the VISTA Browser for pre-computed whole-genome alignments of various organisms.

Related Experiment Videos

  • Submitting user-defined sequences to VISTA servers for comparative analysis.
  • Analyzing a 180 kb interval on human chromosome 5 encoding the KIF3A protein.

    • Main Results:

    • The VISTA site offers multiple comparative genomics tools.
    • Users can browse extensive pre-computed genome alignments.
    • Detailed comparative analysis results are available for specific gene sets, such as cardiovascular genes.

    Conclusions:

    • The VISTA tools provide comprehensive capabilities for comparative genomic analysis.
    • The platform supports both browsing existing alignments and submitting new sequence data.
    • VISTA aids in the identification of functional genomic elements and gene function studies.