Chen Kevin, Pachter Lior
Department of Electrical Engineering and Computer Science, University of California, Berkeley, USA.
PLoS Comput Biol. 2005 Jul;1(2):106-12. doi: 10.1371/journal.pcbi.0010024.
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.
将全基因组鸟枪法测序应用于微生物群落，代表了宏基因组学领域的一项重大进展。宏基因组学是指通过现代基因组分析工具对未培养微生物进行研究。在过去的一年里，已经报道了来自酸性矿生物膜、马尾藻海、明尼苏达农场土壤、三处深海鲸落以及深海沉积物中的原核生物群落的全基因组鸟枪法测序项目，这补充了之前发表的关于海洋和粪便样本中病毒群落的研究工作。对这类新数据的解读带来了各种各样既令人兴奋又颇具难度的生物信息学问题。本综述的目的是通过审视针对其中一些最有趣的计算问题的现有技术和有前景的新方法，向生物信息学领域介绍这个新兴领域。
