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iConcept Journal of Computational and Mathematical Biology
Title
iConcept Journal of Computational and Mathematical Biology
Editor
Maurice Ling
ISSN
2219-1402
Publisher
iConcept Press

iConcept Journal of Computational and Mathematical Biology

Russel and Rao Coefficient is a Suitable Substitute for Dice Coefficient in Studying Restriction Mapped Genetic Distances of Escherichia coli

by Zhu En Chay, Chin How Lee, Kun Cheng Lee, Jack SH Oon and Maurice H. T. Ling

Volume: 1 (2010); Issue: 1

Abstract

Escherichia coli is one of many bacterial inhabitants found in human intestines and any adaptation as a result of mutations may affect its host. A commonly used technique employed to study these mutations is Restriction Fragment Length Polymorphism (RFLP) and is proceeded with a suitable distance coefficient to quantify genetic differences between 2 samples. Dice is considered a suitable distance coefficient in RFLP analyses, while others were left unstudied in its suitability for use. Hence, this study aims to identify substitutes for Dice. Experimental data was obtained by subculturing E. coli for 72 passages in 8 different adaptation media and RFLP profiles analyzed using 20 distance coefficients. Our results suggest that Dennis, Fossum, Matching and Russel and Rao to work as well or better than Dice. Dennis, Matching and Fossum coefficients had highest discriminatory abilities but are limited by the lack of upper or lower boundaries. Russel and Rao coefficient is highly correlated with Dice coefficient (r2 = 0.998), with both higher and lower boundaries, suggesting that Russel and Rao coefficient can be used to substitute Dice coefficient in studying genetic distances in E. coli.

Author Details

Zhu En Chay
School of Chemical and Life Sciences, Singapore Polytechnic, Singapore, Singapore
Chin How Lee
School of Chemical and Life Sciences, Singapore Polytechnic, Singapore, Singapore
Kun Cheng Lee
School of Chemical and Life Sciences, Singapore Polytechnic, Singapore, Singapore
Jack SH Oon
School of Chemical and Life Sciences, Singapore Polytechnic, Singapore, Singapore
Maurice H. T. Ling
Department of Zoology, The University of Melbourne, Australia

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