Fine-tuning the search for microsatellites

Authors:
C. De Ridder;D. G. Kourie;B. W. Watson;T. R. Fourie;P. V. Reyneke
Affiliations:
School of Computing, UNISA, Pretoria, 0002, South Africa and Fastar Research Group, University of Pretoria, Pretoria, 0002, South Africa;Fastar Research Group, University of Pretoria, Pretoria, 0002, South Africa;Fastar Research Group, University of Stellenbosch, Stellenbosch, 7602, South Africa;School of Computing, UNISA, Pretoria, 0002, South Africa;Fastar Research Group, University of Pretoria, Pretoria, 0002, South Africa and Department Radar and Imaging Systems, Denel Dynamics, Irene, 0157, South Africa
Venue:
Journal of Discrete Algorithms
Year:
2013

Citing 9
Cited 0

Introduction to Computer Theory

Introduction to Computer Theory
Introduction To Automata Theory, Languages, And Computation

Introduction To Automata Theory, Languages, And Computation
A first step toward chromosome analysis by compression algorithms

INBS '95 Proceedings of the First International Symposium on Intelligence in Neural and Biological Systems (INBS'95)
Exhaustive whole-genome tandem repeats search

Bioinformatics
STAR: an algorithm to Search for Tandem Approximate Repeats

Bioinformatics
FireμSat: meeting the challenge of detecting microsatellites in DNA

SAICSIT '06 Proceedings of the 2006 annual research conference of the South African institute of computer scientists and information technologists on IT research in developing countries
IMEx

Bioinformatics
Detection of tandem repeats in DNA sequences based on parametric spectral estimation

IEEE Transactions on Information Technology in Biomedicine - Special section on computational intelligence in medical systems
T-REKS

Bioinformatics

Quantified Score

Hi-index	0.00

Visualization

Abstract

The design and implementation is discussed of Fire@mSat"2, an algorithm to detect microsatellites (short approximate tandem repeats) in DNA. The algorithm relies on deterministic finite automata. The parameters are designed to support requirements expressed by molecular biologists in data exploration. By setting the parameters of Fire@mSat"2 as liberally as possible, Fire@mSat"2 is able to detect more microsatellites than all other software algorithms that we have encountered. Furthermore Fire@mSat"2 was found to be faster than all the other algorithms that were investigated for approximate tandem repeat detection. In addition to being fast and accurate, the Fire@mSat"2 algorithm that is described is robust and easily useable.