IMR Press / FBS / Volume 4 / Issue 4 / DOI: 10.2741/S335

Frontiers in Bioscience-Scholar (FBS) is published by IMR Press from Volume 13 Issue 1 (2021). Previous articles were published by another publisher on a subscription basis, and they are hosted by IMR Press on imrpress.com as a courtesy and upon agreement with Frontiers in Bioscience.

Open Access Article
Computational methods for the analysis of tag sequences in metagenomics studies
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1 School of Mathematics, Shandong University, Jinan, Shandong 250100, PR China
2 Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089-2910, USA
3 TNLIST/Department of Automation, Tsinghua University, Beijing 100084, PR China
4 Department of Biological Sciences and Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, CA 90089-2910, USA

*Author to whom correspondence should be addressed.

Academic Editor: Rongling Wu

Front. Biosci. (Schol Ed) 2012, 4(4), 1333–1343; https://doi.org/10.2741/S335
Published: 1 June 2012
(This article belongs to the Special Issue Dynamic genetics and genomics)
Abstract

Metagenomics commonly refers to the study of genetic materials directly derived from environments without culturing. Several ongoing large-scale metagenomics projects related to human and marine life, as well as pedology studies, have generated enormous amounts of data, posing a key challenge for efficient analysis, as we try to 1) understand microbial organism assemblage under different conditions, 2) compare different communities, and 3) understand how microbial organisms associate with each other and the environment.To address such questions, investigators are using new sequencing technologies, including Sanger, Illumina Solexa, and Roche 454, to sequence either particular genes, called tag sequences, mostly 16S or 18S ribosomal RNA sequences or other conserved genes, or whole metagenome shotgun sequences of all the genetic materials in a given community. In this paper, we review computational methods used for the analysis of tag sequences.

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