FireμSat: meeting the challenge of detecting microsatellites in DNA

Authors:
Corne de Riddera;Derrick G. Kourie;Bruce W. Watson
Affiliations:
University of South Africa, South Africa;University of Pretoria, South Africa;University of Pretoria, South Africa
Venue:
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
Year:
2006

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Fine-tuning the search for microsatellites

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Abstract

In the context of this paper, microsatellites refer to consecutive patterns contained by genomic sequences. There are several algorithms that detect microsatellites in DNA, using various computational techniques. In spite of this, there are still molecular biologists who find the output of these algorithms inadequate, and therefore visually scan hardcopy information of sequenced DNA in order to detect microsatellites. The purpose of this paper is threefold: to provide a literature overview of the existing software that detects microsatellites, either directly or indirectly; to compile criteria to which algorithms should comply in order to search effectively for microsatellites; and to motivate the corresponding parameters that have been designed to promote the usability of an analytical, effective algorithm to detect microsatellites. (Details of this algorithm are reported elsewhere.)