Bioinformatics for whole-genome shotgun sequencing of microbial communities

被引：231

作者：

Chen, K ^{[1
]}

Pachter, L

机构：

[1] Univ Calif Berkeley, Dept Elect Engn & Comp Sci, Berkeley, CA 94720 USA

[2] Univ Calif Berkeley, Dept Math, Berkeley, CA 94720 USA

来源：

PLOS COMPUTATIONAL BIOLOGY | 2005年 / 1卷 / 02期

关键词：

D O I：

10.1371/journal.pcbi.0010024

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：106 / 112

页数：7

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