PSP: rapid identification of orthologous coding genes under positive selection across multiple closely related prokaryotic genomes.
PSP: rapid identification of orthologous coding genes under positive selection across multiple closely related prokaryotic genomes.
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PSP：在多个密切相关的原核基因组的正选择下快速鉴定直系同源编码基因
DOI：
10.1186/1471-2164-14-924
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发表时间：
2013-12-27
期刊：
影响因子：
4.4
通讯作者：
Xu P
中科院分区：
文献类型：
--
作者：
Su F;Ou HY;Tao F;Tang H;Xu P
随着许多密切相关的细菌菌株的基因组序列通过深度测序获得，现在有可能研究原核生物微进化的趋势。正选择是微进化的一个亚过程，在这个过程中，一个特定的突变被偏爱，导致等位基因频率不断地向一个方向移动。原核生物基因组的广泛扫描表明，分子水平上的积极选择比预期的要频繁得多。具有显著正选择的基因可能在细菌适应不同环境压力中起关键作用。然而，选择压力分析是计算密集型的，并且难以配置。结果我们设计了一个开放访问的web服务器PSP (Positive Selection analysis for Prokaryotic genomics)，用于对同源编码基因进行进化分析，该服务器专门用于对数十个密切相关的原核生物基因组进行快速比较。值得注意的是，PSP通过分配和丰富KO、GO或COG术语，促进了多层次的功能探索。为了说明这个用户友好的工具，我们分析了大肠杆菌和蜡样芽孢杆菌的基因组，发现在人类感染和抗生素耐药性中起关键作用的几个基因显示出明显的正选择证据。PSP免费提供给所有用户，无需任何登录要求：http://db-mml.sjtu.edu.cn/PSP/。结论spsp最终使研究人员能够快速、方便地进行多原核生物基因组的进化选择分析，并鉴定出可能在宿主-病原体相互作用和/或环境适应中起关键作用的正选择基因。
BackgroundWith genomic sequences of many closely related bacterial strains made available by deep sequencing, it is now possible to investigate trends in prokaryotic microevolution. Positive selection is a sub-process of microevolution, in which a particular mutation is favored, causing the allele frequency to continuously shift in one direction. Wide scanning of prokaryotic genomes has shown that positive selection at the molecular level is much more frequent than expected. Genes with significant positive selection may play key roles in bacterial adaption to different environmental pressures. However, selection pressure analyses are computationally intensive and awkward to configure.ResultsHere we describe an open access web server, which is designated as PSP (Positive Selection analysis for Prokaryotic genomes) for performing evolutionary analysis on orthologous coding genes, specially designed for rapid comparison of dozens of closely related prokaryotic genomes. Remarkably, PSP facilitates functional exploration at the multiple levels by assignments and enrichments of KO, GO or COG terms. To illustrate this user-friendly tool, we analyzedEscherichia coliandBacillus cereusgenomes and found that several genes, which play key roles in human infection and antibiotic resistance, show significant evidence of positive selection. PSP is freely available to all users without any login requirement at: http://db-mml.sjtu.edu.cn/PSP/ .ConclusionsPSP ultimately allows researchers to do genome-scale analysis for evolutionary selection across multiple prokaryotic genomes rapidly and easily, and identify the genes undergoing positive selection, which may play key roles in the interactions of host-pathogen and/or environmental adaptation.
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影响因子：
4.3
作者：
Altenhoff, Adrian M.;Dessimoz, Christophe
通讯作者：
Dessimoz, Christophe
影响因子：
12.3
作者：
Gabaldón T
通讯作者：
Gabaldón T
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3
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Gouveia-Oliveira, Rodrigo;Sackett, Peter W.;Pedersen, Anders G.
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影响因子：
3.2
作者：
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通讯作者：
Bibi, E
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作者：
Lefebure, Tristan;Stanhope, Michael J.
通讯作者：
Stanhope, Michael J.