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Related Experiment Videos

Comparative genomic analysis using the UCSC genome browser.

Donna Karolchik1, Gill Bejerano, Angie S Hinrichs

  • 1UCSC Genome Bioinformatics Group, Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA, USA.

Methods in Molecular Biology (Clifton, N.J.)
|November 13, 2007
PubMed
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Comparative genomics analysis using UCSC tools reveals functional genomic regions. This study details methods for exploring, analyzing, and downloading data from the UCSC Genome Browser for evolutionary insights.

Area of Science:

  • Genomics
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Comparative analysis of DNA sequences across species is crucial for understanding genome function and evolution.
  • The University of California Santa Cruz (UCSC) Genome Bioinformatics group has developed key tools for comparative genomics.
  • The UCSC Genome Browser integrates genomic data and annotation tracks for visualization and analysis.

Purpose of the Study:

  • To describe a procedure for examining genomic regions of interest using UCSC tools.
  • To facilitate the analysis, filtering, and downloading of comparative genomics data.
  • To highlight the utility of the UCSC Genome Browser and Table Browser for research.

Main Methods:

  • Utilizing the UCSC Genome Browser for visualizing pairwise alignments and conservation tracks.

Related Experiment Videos

  • Employing the UCSC Table Browser for querying, analyzing, and downloading genomic data.
  • Examining specific genomic regions to identify orthologous sequences and conserved elements.

    • Main Results:

    • Identification of orthologous regions between species through pairwise alignments.
    • Highlighting potentially functional genomic regions via conservation tracks across multiple species.
    • Successful data extraction and analysis using the UCSC Table Browser.

    Conclusions:

    • The UCSC Genome Browser and Table Browser are powerful, user-friendly tools for comparative genomics research.
    • The described procedure enables efficient examination and data acquisition for functionally significant genomic regions.
    • Comparative genomics analysis aids in understanding evolutionary processes shaping genomes.