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微生物学家专用数据库。

Databases for Microbiologists.

作者信息

Zhulin Igor B

机构信息

Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, and Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA

出版信息

J Bacteriol. 2015 Aug 1;197(15):2458-67. doi: 10.1128/JB.00330-15. Epub 2015 May 26.

Abstract

Databases play an increasingly important role in biology. They archive, store, maintain, and share information on genes, genomes, expression data, protein sequences and structures, metabolites and reactions, interactions, and pathways. All these data are critically important to microbiologists. Furthermore, microbiology has its own databases that deal with model microorganisms, microbial diversity, physiology, and pathogenesis. Thousands of biological databases are currently available, and it becomes increasingly difficult to keep up with their development. The purpose of this minireview is to provide a brief survey of current databases that are of interest to microbiologists.

摘要

数据库在生物学中发挥着越来越重要的作用。它们对基因、基因组、表达数据、蛋白质序列与结构、代谢物与反应、相互作用以及通路等信息进行存档、存储、维护和共享。所有这些数据对微生物学家来说都至关重要。此外,微生物学有其自身处理模式微生物、微生物多样性、生理学和发病机制的数据库。目前有数千个生物学数据库可用,跟上它们的发展变得越来越困难。本小型综述的目的是简要概述微生物学家感兴趣的当前数据库。

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2
SecReT6: a web-based resource for type VI secretion systems found in bacteria.
Environ Microbiol. 2015 Jul;17(7):2196-202. doi: 10.1111/1462-2920.12794.
3
The 2015 Nucleic Acids Research Database Issue and molecular biology database collection.
Nucleic Acids Res. 2015 Jan;43(Database issue):D1-5. doi: 10.1093/nar/gku1241.
4
AromaDeg, a novel database for phylogenomics of aerobic bacterial degradation of aromatics.
Database (Oxford). 2014 Dec 1;2014:bau118. doi: 10.1093/database/bau118. Print 2014.
5
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education.
Nucleic Acids Res. 2015 Jan;43(Database issue):D345-56. doi: 10.1093/nar/gku1214. Epub 2014 Nov 26.
6
The InterPro protein families database: the classification resource after 15 years.
Nucleic Acids Res. 2015 Jan;43(Database issue):D213-21. doi: 10.1093/nar/gku1243. Epub 2014 Nov 26.
7
Gene Ontology Consortium: going forward.
Nucleic Acids Res. 2015 Jan;43(Database issue):D1049-56. doi: 10.1093/nar/gku1179. Epub 2014 Nov 26.
8
Expanded microbial genome coverage and improved protein family annotation in the COG database.
Nucleic Acids Res. 2015 Jan;43(Database issue):D261-9. doi: 10.1093/nar/gku1223. Epub 2014 Nov 26.
9
The BioGRID interaction database: 2015 update.
Nucleic Acids Res. 2015 Jan;43(Database issue):D470-8. doi: 10.1093/nar/gku1204. Epub 2014 Nov 26.
10
OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software.
Nucleic Acids Res. 2015 Jan;43(Database issue):D250-6. doi: 10.1093/nar/gku1220. Epub 2014 Nov 26.

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