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

• Published in: Journal of computer science and technology Vol. 27; no. 2; pp. 225 - 239
• Main Author: 张潮 郑国铝 徐顺福 许东
• Format: Journal Article
• Language: English
• Published: Boston Springer US 01-03-2012; Springer Nature B.V; Department of Computer Science,Christopher S. Bond Life Sciences Center,University of Missouri,Columbia MO 65201,U.S.A.%Department of Agriculture and Environmental Science,Lincoln University,Jefferson City,MO 65101,U.S.A.%Department of Gastroenterology,The First Affiliated Hospital of Nanjing Medical University,Jiangsu 210029,China
• Subjects: Algorithms; Analysis; Artificial Intelligence; Bacteria; Computer Science; Data Structures and Information Theory; E coli; Genomes; Genomics; Information Systems Applications (incl.Internet); Microorganisms; Pathogens; Software Engineering; Studies; Survey; Taxonomy; Theory of Computation; 基因数据; 基础; 宿主; 相互作用; 组数; 细菌鉴定; 表征; 计算问题; bacteria; bacteria-host interaction; metagenomics; 16S rRNA gene; combinatorial entropy; Helicobacter pylori; Faecalibacterium
• ISSN: 1000-9000; 1860-4749
• DOI: 10.1007/s11390-012-1219-y

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.