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Related Experiment Videos

Methods and statistics for combining motif match scores

T L Bailey1, M Gribskov

  • 1San Diego Supercomputer Center, California 92186-9784, USA. tbailey@sdsc.edu

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|July 22, 1998
PubMed
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Combining protein sequence motif scores improves search accuracy. The product of p-values method offers superior statistical significance and classification accuracy compared to other scoring methods.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Position-specific scoring matrices (PSSMs) are crucial for identifying protein sequence motifs.
  • Searching sequence families requires combining scores from multiple motifs.
  • Existing methods for combining motif scores and assessing statistical significance vary in effectiveness.

Purpose of the Study:

  • To evaluate three distinct methods for combining motif match scores.
  • To assess the statistical significance of combined scores.
  • To compare the search quality and statistical accuracy of different combination methods.

Main Methods:

  • Implemented and compared three score combination methods: sum of scores, sum of reduced variates, and product of score p-values.

Related Experiment Videos

  • Evaluated classification accuracy as a measure of search quality.
  • Assessed the accuracy of statistical significance estimates for each method.

    • Main Results:

    • The product of p-values method demonstrated superior performance in both search accuracy and statistical significance estimation.
    • Combining motif scores generally enhanced search accuracy compared to individual motif searches.
    • Method 3 (product of p-values) significantly outperformed the other two methods.

    Conclusions:

    • The product of p-values is the most effective method for combining motif scores in sequence homology searches.
    • Accurate statistical significance estimation is critical for reliable motif-based sequence analysis.
    • The MAST algorithm, using the product of p-values, provides an effective tool for sequence family searching.