P2RP: a Web-based framework for the identification and analysis of regulatory proteins in prokaryotic genomes.
P2RP: a Web-based framework for the identification and analysis of regulatory proteins in prokaryotic genomes.
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DOI：
10.1186/1471-2164-14-269
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发表时间：
2013-04-20
期刊：
影响因子：
4.4
通讯作者：
Whitworth DE
中科院分区：
文献类型：
--
作者：
Barakat M;Ortet P;Whitworth DE
调控蛋白（RPs），如转录因子（TFs）和双组分系统（TCS）蛋白控制原核细胞如何响应其外部和/或内部状态的变化。TFs和TCSs的鉴定和注释是非常有意义的，基因组间比较常常因注释标准不同而混淆。研究人员需要一种用户友好、快速和方便的工具来克服基因组序列之间注释的固有可变性。我们开发了web服务器P2RP（预测原核调节蛋白），使用户能够在他们感兴趣的序列中识别和注释TFs和TCS蛋白。用户可以输入氨基酸或基因组DNA序列，并对其中的预测蛋白质进行扫描以确定其是否拥有DNA结合结构域和/或TCS结构域。使用集成的软件管道，以这种方式识别的rp被分类为家族，明确地注释，并生成其特征的详细描述。然后可以以用户指定的格式输出P2RP结果。生物学家越来越需要快速和直观可用的工具，这就是为什么P2RP被开发为一个交互式系统的原因。在协助实验生物学家查询新序列数据的同时，希望将P2RP构建到基因组注释管道和重新注释过程中，以提高公开基因组序列中RP注释的一致性。P2RP是第一个用于预测和分析用户序列中RP蛋白的公开工具。该服务器是免费提供的，可以在http://www.p2rp.org上与文档一起访问。
Regulatory proteins (RPs) such as transcription factors (TFs) and two-component system (TCS) proteins control how prokaryotic cells respond to changes in their external and/or internal state. Identification and annotation of TFs and TCSs is non-trivial, and between-genome comparisons are often confounded by different standards in annotation. There is a need for user-friendly, fast and convenient tools to allow researchers to overcome the inherent variability in annotation between genome sequences. We have developed the web-server P2RP (Predicted Prokaryotic Regulatory Proteins), which enables users to identify and annotate TFs and TCS proteins within their sequences of interest. Users can input amino acid or genomic DNA sequences, and predicted proteins therein are scanned for the possession of DNA-binding domains and/or TCS domains. RPs identified in this manner are categorised into families, unambiguously annotated, and a detailed description of their features generated, using an integrated software pipeline. P2RP results can then be outputted in user-specified formats. Biologists have an increasing need for fast and intuitively usable tools, which is why P2RP has been developed as an interactive system. As well as assisting experimental biologists to interrogate novel sequence data, it is hoped that P2RP will be built into genome annotation pipelines and re-annotation processes, to increase the consistency of RP annotation in public genomic sequences. P2RP is the first publicly available tool for predicting and analysing RP proteins in users’ sequences. The server is freely available and can be accessed along with documentation at http://www.p2rp.org.
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