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Selecting representative model micro-organisms

Citation

Holland, BR and Schmid, J, Selecting representative model micro-organisms, BMC Microbiology, 5, (May) pp. 1-11. ISSN 1471-2105 (2005) [Refereed Article]


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Copyright Statement

2005 Holland and Schmid; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

DOI: doi:10.1186/1471-2180-5-26

Abstract

Background Micro-biological research relies on the use of model organisms that act as representatives of their species or subspecies, these are frequently well-characterized laboratory strains. However, it has often become apparent that the model strain initially chosen does not represent important features of the species. For micro-organisms, the diversity of their genomes is such that even the best possible choice of initial strain for sequencing may not assure that the genome obtained adequately represents the species. To acquire information about a species' genome as efficiently as possible, we require a method to choose strains for analysis on the basis of how well they represent the species. Results We develop the Best Total Coverage (BTC) method for selecting one or more representative model organisms from a group of interest, given that rough genetic distances between the members of the group are known. Software implementing a "greedy" version of the method can be used with large data sets, its effectiveness is tested using both constructed and biological data sets. Conclusion In both the simulated and biological examples the greedy-BTC method outperformed random selection of model organisms, and for two biological examples it outperformed selection of model strains based on phylogenetic structure. Although the method was designed with microbial species in mind, and is tested here on three microbial data sets, it will also be applicable to other types of organism.

Item Details

Item Type:Refereed Article
Research Division:Mathematical Sciences
Research Group:Applied Mathematics
Research Field:Biological Mathematics
Objective Division:Expanding Knowledge
Objective Group:Expanding Knowledge
Objective Field:Expanding Knowledge in the Biological Sciences
Author:Holland, BR (Associate Professor Barbara Holland)
ID Code:63074
Year Published:2005
Web of Science® Times Cited:5
Deposited By:Mathematics
Deposited On:2010-04-13
Last Modified:2012-03-06
Downloads:278 View Download Statistics

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