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Poly: a quantitative analysis tool for simple sequence repeat (SSR) tracts in DNA.

Jeff W Bizzaro1, Kenneth A Marx

  • 1Bioinformatics Organization, Inc, 28 Pope Street, Hudson, MA 01749 USA. jeff@bioinformatics.org

BMC Bioinformatics
|June 7, 2003
PubMed
Summary
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A new program, Poly, identifies simple sequence repeats (SSRs) and analyzes their frequencies and lengths. This tool offers quantitative methods for SSR analysis, advancing biological research.

Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Simple sequence repeats (SSRs), also known as microsatellites, are common DNA sequences.
  • SSR tracts, ranging from mononucleotides to trinucleotides and beyond, can exceed six repeating units.
  • Current computational tools for SSR identification often lack quantitative analysis capabilities for frequencies and tract lengths.

Purpose of the Study:

  • To develop a computational tool for identifying and quantitatively analyzing simple sequence repeats (SSRs).
  • To address the limitations of existing programs in analyzing SSR frequencies and tract lengths.

Main Methods:

  • Development of a computer program named Poly.
  • Implementation of quantitative methods for analyzing SSR tract frequencies and lengths.
  • Utilizing a flexible object model and data structure within the Poly program.

Related Experiment Videos

Main Results:

  • Poly successfully identifies SSR tracts within DNA sequences.
  • The program provides quantitative analysis of SSR frequencies and tract lengths.
  • Generated data from Poly can be utilized for advanced analyses.

Conclusions:

  • Poly introduces novel, non-standard quantitative methods for SSR analysis.
  • The program's flexible design supports sophisticated downstream analyses.
  • Poly enhances the study of SSRs through its advanced analytical capabilities.