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Improved tools for DNA comparison and clustering

J D Parsons1

  • 1Genome Sequencing Center, Washington University School of Medicine, St Louis, MO 63108, USA. jparsons@watson.wustl.edu

Computer Applications in the Biosciences : CABIOS
|December 1, 1995
PubMed
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New DNA sequence clustering tools (ICAtools) enhance database comprehension and compression. These programs efficiently cluster genomic DNA, EST projects, and large databases, improving data management and analysis.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • DNA sequence clustering aids in understanding, summarizing, and compressing large DNA sequence databases.
  • Existing tools were limited, primarily focusing on cDNA sequence comparison and clustering.

Purpose of the Study:

  • To introduce and describe three novel DNA sequence clustering programs: ICAass, N2tool, and ICAmatches.
  • To demonstrate their enhanced capabilities for clustering genomic DNA fragments, EST projects, and entire DNA databases.

Main Methods:

  • Development of three distinct programs: ICAass for database compression and querying, N2tool for sensitive genomic fragment clustering, and ICAmatches for multiple alignment summaries.
  • Utilizing a common, memory-frugal index format and direct acceptance of most DNA sequence formats for user convenience.

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Main Results:

  • ICAass successfully compressed the EMBL database and offers the fastest database querying.
  • N2tool provides rapid and sensitive clustering of genomic fragments, aiding in the detection of contaminating sequences.
  • ICAmatches introduces a novel alignment style for presenting multiple alignment summaries.

Conclusions:

  • The ICAtools suite offers significant advancements in DNA sequence database management and analysis.
  • These tools enhance efficiency, sensitivity, and usability for various genomics research applications.