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Review of tandem repeat search tools: a systematic approach to evaluating algorithmic performance
Kian Guan Lim1, Chee Keong Kwoh, Li Yang Hsu
1Division of Software and Information Systems, School of Computer Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798. kglim1@e.ntu.edu.sg
Briefings in Bioinformatics
|June 1, 2012
Summary
This review clarifies how different algorithms and parameter settings affect tandem repeat detection tools, aiding researchers in selecting the best methods for genetic analysis and disease research.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Tandem repeats are prevalent in eukaryotic genomes and linked to genetic diseases.
- Numerous tools exist for tandem repeat detection, but results vary due to algorithmic differences and parameter settings.
Purpose of the Study:
- To systematically separate algorithmic aspects from parameter setting influences in tandem repeat search tools.
- To enhance understanding of algorithmic performance, constraints, and selection criteria for these tools.
Main Methods:
- Algorithmic comparison of tandem repeat search tools.
- Analysis of parameter setting impacts on search results.
Main Results:
- Identified key algorithmic differences influencing tool performance.
- Demonstrated how parameter settings affect the variability of results.
Conclusions:
- A clear distinction between algorithm and parameter settings is crucial for evaluating tandem repeat detection tools.
- This systematic approach aids researchers in selecting appropriate tools for accurate genetic analysis.
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