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A note about computing all local alignments

W Miller1, M Boguski

  • 1Department of Computer Science and Engineering, Pennsylvania State University, University Park 16802.

Computer Applications in the Biosciences : CABIOS
|July 1, 1994
PubMed
Summary
This summary is machine-generated.

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This note identifies a flaw in Barton's sequence alignment algorithm. The efficient method for finding local sequence alignments sometimes misses significant matches, despite claims otherwise.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Sequence Analysis

Background:

  • G. Barton recently proposed an efficient algorithm for identifying locally optimal sequence alignments.
  • The algorithm claims to find all significant sequence matches between two sequences.

Purpose of the Study:

  • To identify and explain a deficiency in Barton's sequence alignment algorithm.
  • To address the algorithm's failure to detect all significant sequence matches.

Main Methods:

  • Analysis of Barton's proposed algorithm.
  • Identification of failure cases in the algorithm's execution.

Main Results:

  • The algorithm, while efficient, does not consistently detect all significant local sequence alignments.

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  • Specific scenarios where the algorithm fails to identify matches are detailed.

    • Conclusions:

    • Barton's algorithm has limitations and may not be as comprehensive as initially claimed.
    • Further refinement or alternative approaches may be needed for complete detection of significant sequence alignments.