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Journal of Computer Science and Technology 2010, Vol. 25 Issue (1) :71-81    DOI:
Special Issue on Computational Challenges from Modern Molecular Biology Current Issue | Archive | Adv Search << Previous Articles | Next Articles >>
Metagenomics: Facts and Artifacts, and Computational Challenges
John C. Wooley1 and Yuzhen Ye2 (叶玉珍)
1Center for Research on BioSystems, Calit2, University of Califormia San Diego, La Jolla, CA 92093, U.S.A.
2School of Informatics and Computing, Indiana University, Bloomington, Indiana, 47408, U.S.A.

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Metagenomics is the study of microbial communities sampled directly from their natural environment, without prior culturing. By enabling an analysis of populations including many (so-far) unculturable and often unknown microbes, metagenomics is revolutionizing the field of microbiology, and has excited researchers in many disciplines that could benefit from the study of environmental microbes, including those in ecology, environmental sciences, and biomedicine. Specific computational and statistical tools have been developed for metagenomic data analysis and comparison. New studies, however, have revealed various kinds of artifacts present in metagenomics data caused by limitations in the experimental protocols and/or inadequate data analysis procedures, which often lead to incorrect conclusions about a microbial community. Here, we review some of the artifacts, such as overestimation of species diversity and incorrect estimation of gene family frequencies, and discuss emerging computational approaches to address them. We also review potential challenges that metagenomics may encounter with the extensive application of next-generation sequencing (NGS) techniques.

Articles by authors
John C. Wooley
Yuzhen Ye
Keywordsmetagenomics    next-generation sequencing (NGS)    taxonomic/functional profiling    statistical approaches    comparative metagenomics     
Received 2009-08-30;

This work is supported by NIH under Grant No. 1R01HG004908-01, NSF of USA under Grant No. DBI-0845685 (YY), and also the Gordon and Betty Moore Foundation for the Community Cyberinfrastructure for Marine Microbial Ecological Research and Analysis (CAMERA) Project (JW).

Cite this article:   
John C. Wooley and Yuzhen Ye.Metagenomics: Facts and Artifacts, and Computational Challenges[J]  Journal of Computer Science and Technology, 2010,V25(1): 71-81
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