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The Saccharomyces Genome Database: Advanced Searching Methods and Data Mining.

J Michael Cherry1

  • 1Department of Genetics, Stanford University School of Medicine, Stanford, California 94305-5120.

Cold Spring Harbor Protocols
|December 4, 2015
PubMed
Summary
This summary is machine-generated.

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The Saccharomyces Genome Database (SGD) provides comprehensive yeast genomic data. New tools, YeastMine and SPELL, enhance data exploration and analysis for researchers.

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • The Saccharomyces Genome Database (SGD) is a central resource for yeast genomic information.
  • SGD contains data on protein-coding genes, noncoding RNA genes, and other chromosomal features.
  • Access to SGD data is typically through gene names, keywords, or sequence similarity searches.

Purpose of the Study:

  • To describe advanced data exploration tools for the Saccharomyces Genome Database.
  • To introduce YeastMine for interactive, structured data searching.
  • To present SPELL for analyzing yeast gene expression data from microarrays.

Main Methods:

  • Utilizing YeastMine for advanced querying of SGD's structured data.
  • Employing SPELL for the exploration of microarray expression data.

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  • Leveraging BLAST for gene identification using DNA or protein sequences.

    • Main Results:

    • YeastMine offers an interactive platform for complex data retrieval.
    • SPELL enables efficient analysis of serial patterns in gene expression levels.
    • SGD provides multiple entry points for accessing curated yeast genomic information.

    Conclusions:

    • YeastMine and SPELL significantly enhance the utility of the Saccharomyces Genome Database.
    • These tools empower researchers to conduct more sophisticated analyses of yeast genomic and expression data.
    • SGD remains a vital, evolving resource for the yeast research community.