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Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching
1San Diego Supercomputer Center, P.O. Box 85608, San Diego, CA 92186-9784, USA.
Computers & Chemistry
|March 1, 1996
Summary
This study applies receiver operating characteristic (ROC) analysis to protein sequence comparison. Optimal database searches require specific parameters, differing from alignment conditions, particularly regarding gap penalties and PAM distance.
Area of Science:
- Bioinformatics
- Computational Biology
- Biotechnology
Background:
- Sequence comparison is crucial in bioinformatics.
- Traditional methods may not fully capture optimal search parameters.
- Receiver Operating Characteristic (ROC) analysis offers a quantitative diagnostic measure.
Purpose of the Study:
- To adapt ROC analysis for sequence comparison.
- To investigate the impact of scoring tables and gap penalties on database searches.
- To determine optimal parameters for protein sequence database searching.
Main Methods:
- Application of ROC analysis to sequence comparison.
- Evaluation of scoring tables and gap penalties (initiation and extension).
- Database searches using the Smith-Waterman algorithm on protein families (ferredoxins, lysR, sigma-factors).
Main Results:
- Protein sequence families exhibit unique characteristics.
- Optimal PAM distance for database searches is approximately 200 PAM.
- Length-independent gap penalties (initiation) are critical, peaking at 20-24.
- Length-dependent gap penalties (extension) have minimal impact.
Conclusions:
- Optimal conditions for sequence alignment and database searching are distinct.
- ROC analysis provides valuable insights into sequence comparison parameters.
- Database search effectiveness is influenced more by gap initiation than extension penalties.
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