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e-Science: relieving bottlenecks in large-scale genome analyses

Nature Reviews Microbiology volume 6, pages 948–954 (2008)Cite this article

Abstract

The development of affordable, high-throughput sequencing technology has led to a flood of publicly available bacterial genome-sequence data. The availability of multiple genome sequences presents both an opportunity and a challenge for microbiologists, and new computational approaches are needed to extract the knowledge that is required to address specific biological problems and to analyse genomic data. The field of e-Science is maturing, and Grid-based technologies can help address this challenge.

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Figure 1: Publicly available bacterial genomes.
Figure 2: Analysis of the Bacillus subtilis secretome as an in silico experiment.
Figure 3: A heat map that shows the prevalence of secreted protein families across 12 Bacillus species.

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Acknowledgements

The authors acknowledge funding from the UK Engineering and Physical Sciences Research Council and Non-linear Dynamics for a CASE (collaborative awards in science and engineering) studentship to T.C., from Research Councils UK for a fellowship to J.H. and from the European Union (Bacell Health; grant number LSH-2002-1.1.0-1).

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Authors and Affiliations

  1. Tracy Craddock, Jennifer Hallinan and Anil Wipat are at the School of Computing Science, Claremont Tower, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.,

    Tracy Craddock, Jennifer Hallinan & Anil Wipat

  2. Colin R. Harwood is at the Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.,

    Colin R. Harwood

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  1. Tracy Craddock
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  2. Colin R. Harwood
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Correspondence to Colin R. Harwood.

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DATABASES

Entrez Genome Project

Staphylococcus aureus

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EMBL–EBI (Genome Pages — Bacteria)

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Craddock, T., Harwood, C., Hallinan, J. et al. e-Science: relieving bottlenecks in large-scale genome analyses. Nat Rev Microbiol 6, 948–954 (2008). https://doi.org/10.1038/nrmicro2031

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