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Physiol Mol Biol Plants. 2012 Jan;18(1):11-9. doi: 10.1007/s12298-011-0098-y. Epub 2011 Dec 23.

Searching microsatellites in DNA sequences: approaches used and tools developed.

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  • 1University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C Dwarka, New Delhi, 110075 India ; Molecular Biology and Genetic Engineering Laboratory, Defence Institute of Bio Energy Research, Goraparao, Haldwani, 263139 India.


Microsatellite instability associated genomic activities and evolutionary changes have led to a renewed focus on microsatellite research. In last decade, a number of microsatellite mining tools have been introduced based on different computational approaches. The choice is generally made between slow but exhaustive dynamic programming based approaches, or fast and incomplete heuristic methods. Tools based on stochastic approaches are more popular due to their simplicity and added ornamental features. We have performed a comparative evaluation of the relative efficiency of some microsatellite search tools with their default settings. The graphical user interface, the statistical analysis of the output and ability to mine imperfect repeats are the most important criteria in selecting a tool for a particular investigation. However, none of the available tools alone provides complete and accurate information about microsatellites, and a lot depends on the discretion of the user.


Deterministic approaches; Microsatellites; Mining tools; Stochastic models

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