Review of tandem repeat search tools: a systematic approach to evaluating algorithmic performance.
The prevalence of tandem repeats in eukaryotic genomes and their association with a number of genetic diseases has raised considerable interest in locating these repeats. Over the last 10-15 years, numerous tools have been developed for searching tandem repeats, but differences in the search algorithms adopted and difficulties with parameter settings have confounded many users resulting in widely varying results. In this review, we have systematically separated the algorithmic aspect of the search tools from the influence of the parameter settings. We hope that this will give a better understanding of how the tools differ in algorithmic performance, their inherent constraints and how one should approach in evaluating and selecting them.
Division of Software and Information Systems, School of Computer Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798. kglim1@e.ntu.edu.sg
Kian Guan
KG
Lim
Chee Keong
CK
Kwoh
Li Yang
LY
Hsu
Adrianto
A
Wirawan
D000465:Algorithms; D000818:Animals; D019295:Computational Biology; D030561:Databases, Nucleic Acid / Q000706:statistics & numerical data; D006801:Humans; D057386:Search Engine; D017422:Sequence Analysis, DNA / Q000706:statistics & numerical data; D020080:Tandem Repeat Sequences / Q000235:genetics