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Rapid motif compliance scoring with match weight sets
1ZymoGenetics, Inc., Seattle, WA 98105.
Computer Applications in the Biosciences : CABIOS
|February 1, 1993
Summary
The MOTIF program enhances biological sequence analysis by combining weight matrix scoring with a fast search algorithm. This allows for flexible and efficient motif matching without compromising accuracy.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Current motif matching algorithms often trade accuracy for speed.
- Weight matrix scoring provides generality but can be computationally intensive.
Purpose of the Study:
- To develop a motif matching program (MOTIF) that balances speed and generality.
- To enable flexible motif searching with enhanced performance.
Main Methods:
- Implemented a weight matrix scoring system.
- Utilized a rapid, backtracking tree-search algorithm for motif compliance.
- Allowed for 'inviolate' positions within motifs for exact matching.
- Supported various regular expression formats and sequence/motif libraries.
- Enabled optional nucleic acid translation for peptide motif analysis.
Main Results:
- Achieved greatly enhanced performance in motif matching.
- Maintained generality of weight matrix scoring.
- Provided flexibility in defining motifs, including inviolate positions.
- Facilitated versatile use of sequence and motif libraries.
Conclusions:
- MOTIF offers a powerful and efficient solution for motif discovery in biological sequences.
- The program's flexibility supports diverse applications in bioinformatics.
- Optimized performance without sacrificing the accuracy of weight matrix scoring.