Comparative analysis of environmental sequences: potential and challenges

Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
Konrad U FoerstnerP Bork

Abstract

Environmental sequencing, also dubbed metagenomics, is increasingly being used to obtain insights into organismal communities in diverse habitats, and has a variety of potential applications foreseeable in biotechnology and medicine. The first public large-scale data provide already a wealth of information hidden in vast amounts of fragmented pieces of DNA from unknown species residing in these environments. Comparative sequence analysis is essential for the interpretation of such data. However, different layers of complexity that are intrinsic to each sample require the establishment of some baselines for comparison: how to normalize for the differences in phylogenetic and functional diversity, how to avoid biases from incomplete data, and how to deal with differences in species dominance or genome sizes? Here we discuss a few of these items and delineate some simple discriminative sequence properties for four distinct habitats.

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Citations

Apr 17, 2007·Microbial Ecology·Dawn Field, Nikos Kyrpides
Mar 10, 2006·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·David T JonesJanet M Thornton
Jun 10, 2009·Journal of Bioinformatics and Computational Biology·Yuzhen Ye, Haixu Tang
Apr 30, 2008·BMC Bioinformatics·Chon-Kit Kenneth ChanSen-Lin Tang
Jan 25, 2008·BMC Bioinformatics·Patrick D Schloss, Jo Handelsman
Jan 17, 2007·Genome Biology·Jeroen RaesPeer Bork
May 21, 2010·PloS One·Bo HuYing-jin Yuan
May 29, 2008·Future Microbiology·Grigoris D AmoutziasDimitris Mossialos
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Dec 7, 2007·Studies in History and Philosophy of Biological and Biomedical Sciences·John Dupré, Maureen A O'Malley

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