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Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities

Chen, Kevin and Pachter, Lior (2005) Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities. PLoS Computational Biology, 1 (2). Art. No. e24. ISSN 1553-734X. PMCID PMC1185649. doi:10.1371/journal.pcbi.0010024. https://resolver.caltech.edu/CaltechAUTHORS:20170308-124940796

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Abstract

The application of whole-genome shotgun sequencing to microbial communities represents a major development in metagenomics, the study of uncultured microbes via the tools of modern genomic analysis. In the past year, whole-genome shotgun sequencing projects of prokaryotic communities from an acid mine biofilm, the Sargasso Sea, Minnesota farm soil, three deep-sea whale falls, and deep-sea sediments have been reported, adding to previously published work on viral communities from marine and fecal samples. The interpretation of this new kind of data poses a wide variety of exciting and difficult bioinformatics problems. The aim of this review is to introduce the bioinformatics community to this emerging field by surveying existing techniques and promising new approaches for several of the most interesting of these computational problems.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1371/journal.pcbi.0010024DOIArticle
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.0010024PublisherArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1185649/PubMed CentralArticle
ORCID:
AuthorORCID
Pachter, Lior0000-0002-9164-6231
Additional Information: © 2005 Chen and Pachter. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Published: July 12, 2005. We thank Eric Allen, Jill Banfield, Susannah Tringe, and Gene Tyson for introducing us to the field of metagenomics and for helpful discussions while preparing the manuscript. We also thank Richard Karp and Satish Rao for useful discussions on bioinformatics issues, and the anonymous reviewers for their comments on an earlier version of this paper. Some of the data we have used were provided by JGI and EMBL. KC was supported by National Science Foundation (NSF) grant EF 03–31494. LP was supported by a Sloan Research Fellowship, NSF grant CCF 03–47992, and National Institutes of Health grant R01-HG02362–03.
Funders:
Funding AgencyGrant Number
NSFEF-0331494
Alfred P. Sloan FoundationUNSPECIFIED
NSFCCF-0347992
NIHR01-HG02362–03
Issue or Number:2
PubMed Central ID:PMC1185649
DOI:10.1371/journal.pcbi.0010024
Record Number:CaltechAUTHORS:20170308-124940796
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20170308-124940796
Official Citation:Chen K, Pachter L (2005) Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities. PLoS Comput Biol 1(2): e24. doi:10.1371/journal.pcbi.0010024
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:74902
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:08 Mar 2017 21:15
Last Modified:15 Nov 2021 16:29

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