Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence
1Department of Molecular Biophysics and Biochemistry, 266 Whitney Avenue, Yale University, PO Box 208114, New Haven, CT 06520, USA. Mark.Gerstein@yale.ed
Bioinformatics (Oxford, England)
|October 28, 1998
Summary
Transitive sequence matching enhances protein sequence comparison by uncovering indirect relationships. This method reveals 5% more structural similarities than direct comparison, with minimal false positives.
Area of Science:
- Computational biology
- Bioinformatics
- Structural biology
Background:
- Transitive sequence matching offers greater sensitivity than direct pairwise comparison by re-querying results.
- The precise improvement in sensitivity has not been previously quantified.
Purpose of the Study:
- To comprehensively measure the improvement in sequence comparison sensitivity provided by transitive matching.
- To quantify the fraction of known structural relationships that transitive matching can uncover beyond direct comparison.
Main Methods:
- Utilized the scop classification of protein structure as a test set for known structural relationships.
- Derived 'baseline sets' of sequence pairs with structural similarity not detectable by direct comparison.
- Employed standard sequence comparison protocols (FASTA, e-value cut-off 0.001) to assess transitive matching performance.
Main Results:
- Transitive sequence matching indirectly linked 5% (86 out of 1742) of sequence pairs with structural similarity undetectable by direct comparison.
- False positive rates were minimal.
- For closely structurally aligned pairs (better than 2.6 Å RMS), transitive matching identified 9% (62 out of 862) of the baseline set pairs.
Conclusions:
- Transitive sequence matching provides a measurable increase in sensitivity for uncovering structural relationships between distantly related proteins.
- The method is effective even for closely related proteins, though the coverage is lower than for more distant relationships.
- The findings support the utility of transitive sequence matching for enhancing sequence comparison in bioinformatics.
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