PhyMet2: a database and toolkit for phylogenetic and metabolic analyses of methanogens
PhyMet2: a database and toolkit for phylogenetic and metabolic analyses of methanogens
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PhyMet2：用于产甲烷菌系统发育和代谢分析的数据库和工具包
DOI：
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发表时间：
2018
影响因子：
3.3
通讯作者：
Łukaszewicz Marcin
中科院分区：
文献类型：
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作者：
Burdukiewicz Michał;Przemysław Gagat;Sławomir Jabłoński;J. Chilimoniuk;M. Gaworski;P. Mackiewicz;Łukaszewicz Marcin
广泛的宏基因组学分析已经揭示了微生物世界的巨大生物多样性以及对它的了解有多少。我们对微生物的基本知识来自于在实验室条件下分离和培养微生物的困难，这对于描述它们的表型是必要的，除其他外，用于生物技术目的。未充分研究的生态系统的一个重要组成部分是产甲烷菌，古细菌产生一种强大的温室效应气体甲烷。因此，我们创建了PhyMet 2，这是第一个将产甲烷菌及其培养条件的描述与遗传信息相结合的数据库。该数据库包含一套实用程序，便于交互式数据浏览，数据比较，同源性探索和搜索序列同源物。该数据库最独特的功能是网络服务器MethanoGram，通过基于16S RNA序列预测产甲烷菌的最佳培养条件，可以大大减少搜索产甲烷菌最佳培养条件的时间和成本。该数据库将帮助许多研究人员探索产甲烷菌及其在生物技术过程中的应用。具有MethanoGram预测器的PhyMet2可在http://metanogen.biotech.uni.wroc.pl上获得。
The vast biodiversity of the microbial world and how little is known about it, has already been revealed by extensive metagenomics analyses. Our rudimentary knowledge of microbes stems from difficulties concerning their isolation and culture in laboratory conditions, which is necessary for describing their phenotype, among other things, for biotechnological purposes. An important component of the understudied ecosystems is methanogens, archaea producing a potent greenhouse-effect gas methane. Therefore, we created PhyMet2 , the first database that combines descriptions of methanogens and their culturing conditions with genetic information. The database contains a set of utilities that facilitate interactive data browsing, data comparison, phylogeny exploration and searching for sequence homologues. The most unique feature of the database is the web server MethanoGram, which can be used to significantly reduce the time and cost of searching for the optimal culturing conditions of methanogens by predicting them based on 16S RNA sequences. The database will aid many researchers in exploring the world of methanogens and their applications in biotechnological processes. PhyMet2 with the MethanoGram predictor is available at http://metanogen.biotech.uni.wroc.pl.