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Related Experiment Videos

A RAPID algorithm for sequence database comparisons: application to the identification of vector contamination in the

C Miller1, J Gurd, A Brass

  • 1School of Biological Sciences, 2.205 The Stopford Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK.

Bioinformatics (Oxford, England)
|March 25, 1999
PubMed
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A new sequence comparison algorithm separates word matching and alignment, enabling faster and more sensitive DNA sequence analysis. This approach significantly improves the detection of vector contamination in sequence databases.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomic Data Analysis

Background:

  • Traditional sequence comparison algorithms like BLAST use word matching to seed alignments.
  • Assessing sequence similarity often relies on these seeded alignments.
  • Vector contamination in DNA databases is a persistent issue.

Purpose of the Study:

  • To develop a novel sequence comparison algorithm that separates word-matching from sequence-alignment.
  • To create a fast and sensitive method for identifying vector contamination in DNA sequence databases.
  • To offer users flexibility in choosing alignment methods without compromising similarity search.

Main Methods:

  • Developed three algorithms: RAPID (word search), PHAT, and SPLAT (alignment).
  • Utilized word frequencies and probabilities to enhance significance in word matching.

Related Experiment Videos

  • Employed Receiver Operator Characteristic (ROC) analysis to determine optimal parameters and score thresholds.

    • Main Results:

    • The new algorithm implementation is approximately ten times faster than BLAST.
    • Achieved significant performance gains through the formal separation of word searching and alignment.
    • Identified vector contamination rates of 0.27% in the EMBL EST subset and 0.86% in a specific EST dataset.

    Conclusions:

    • The developed algorithm provides a rapid and sensitive solution for detecting vector contamination.
    • The modular design allows for user-selectable alignment strategies.
    • The findings highlight the prevalence of vector contamination in public sequence databases.