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

Authors

  • Chao Zhang
    • Department of Computer Science, Christopher S. Bond Life Sciences CenterUniversity of Missouri
  • Guolu Zheng
    • Department of Agriculture and Environmental ScienceLincoln University
  • Shun-Fu Xu
    • Department of GastroenterologyThe First Affiliated Hospital of Nanjing Medical University
    • Department of Computer Science, Christopher S. Bond Life Sciences CenterUniversity of Missouri
Survey

DOI: 10.1007/s11390-012-1219-y

Cite this article as:
Zhang, C., Zheng, G., Xu, S. et al. J. Comput. Sci. Technol. (2012) 27: 225. doi:10.1007/s11390-012-1219-y

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

bacteriabacteria-host interactionmetagenomics16S rRNA geneFaecalibacteriumHelicobacter pyloricombinatorial entropy

Supplementary material

11390_2012_1219_MOESM1_ESM.pdf (86 kb)
(PDF 86.2 kb)

Copyright information

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