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Related Experiment Videos

Kangaroo--a pattern-matching program for biological sequences.

Doron Betel1, Christopher W V Hogue

  • 1Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada. betel@mshri.on.ca

BMC Bioinformatics
|August 2, 2002
PubMed
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Biologists can now easily identify DNA and protein patterns using Kangaroo, a new web-based tool. This regular expression pattern-matching program aids in discovering potential mutation sites and genetic targets in various organisms.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Biologists require tools to search sequence patterns in databases for identifying proteins or genes.
  • Existing databases often lack straightforward query tools for simple pattern searches like transcription binding sites or repetitive DNA sequences.
  • Simple pattern-matching searches can yield significant biological insights.

Purpose of the Study:

  • To present a regular expression pattern-matching tool for identifying short repetitive DNA sequences in human coding regions.
  • To facilitate the identification of potential mutation sites in mismatch repair deficient cells.

Main Methods:

  • Development of Kangaroo, a web-based regular expression pattern-matching program.
  • The program searches for patterns in DNA, protein, or coding region sequences across ten organisms.

Related Experiment Videos

  • Kangaroo supports queries of unrestricted length and complexity.

    • Main Results:

    • Kangaroo is accessible online at http://bioinfo.mshri.on.ca/kangaroo/.
    • The source code for Kangaroo is freely available at http://sourceforge.net/projects/slritools/.
    • The tool was successfully used to identify potential genetic targets in a human colorectal cancer variant with high mutation frequency in coding regions with mononucleotide repeats.

    Conclusions:

    • Simple pattern-matching applications are valuable research tools.
    • Kangaroo can identify potential genetic targets in cancer variants.
    • The tool aids in understanding mutations in coding regions with repetitive sequences.