Journal of Computer Science and Technology

, Volume 27, Issue 2, pp 225–239

Computational Challenges in Characterization of Bacteria and Bacteria-Host Interactions Based on Genomic Data

Survey

Abstract

With the rapid development of next-generation sequencing technologies, bacterial identification becomes a very important and essential step in processing genomic data, especially for metagenomic data. Many computational methods have been developed and some of them are widely used to address the problems in bacterial identification. In this article we review the algorithms of these methods, discuss their drawbacks, and propose future computational methods that use genomic data to characterize bacteria. In addition, we tackle two specific computational problems in bacterial identification, namely, the detection of host-specific bacteria and the detection of disease-associated bacteria, by offering potential solutions as a starting point for those who are interested in the area.

Keywords

bacteria bacteria-host interaction metagenomics 16S rRNA gene Faecalibacterium Helicobacter pylori combinatorial entropy 

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Copyright information

© Springer Science+Business Media, LLC & Science Press, China 2012

Authors and Affiliations

  1. 1.Department of Computer Science, Christopher S. Bond Life Sciences CenterUniversity of MissouriColumbiaU.S.A.
  2. 2.Department of Agriculture and Environmental ScienceLincoln UniversityJefferson CityU.S.A.
  3. 3.Department of GastroenterologyThe First Affiliated Hospital of Nanjing Medical UniversityJiangsuChina

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