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AGONOTES: A Robot Annotator for Argonaute Proteins.
Interdisciplinary Sciences: Computational Life Sciences ( IF 4.8 ) Pub Date : 2019-11-18 , DOI: 10.1007/s12539-019-00349-4
Lixu Jiang 1 , Min Yu 1 , Yuwei Zhou 1 , Zhongjie Tang 1 , Ning Li 1 , Juanjuan Kang 1 , Bifang He 1, 2 , Jian Huang 1
Affiliation  

The argonaute protein (Ago) exists in almost all organisms. In eukaryotes, it functions as a regulatory system for gene expression. In prokaryotes, it is a type of defense system against foreign invasive genomes. The Ago system has been engineered for gene silencing and genome editing and plays an important role in biological studies. With an increasing number of genomes and proteomes of various microbes becoming available, computational tools for identifying and annotating argonaute proteins are urgently needed. We introduce AGONOTES (Argonaute Notes). It is a web service especially designed for identifying and annotating Ago. AGONOTES uses the BLASTP similarity search algorithm to categorize all submitted proteins into three groups: prokaryotic argonaute protein (pAgo), eukaryotic argonaute protein (eAgo), and non-argonaute protein (non-Ago). Argonaute proteins can then be aligned to the corresponding standard set of Ago sequences using the multiple sequence alignment program MUSCLE. All functional domains of Ago can further be curated from the alignment results and visualized easily through Bio::Graphic modules in the BioPerl bundle. Compared with existing tools such as CD-Search and available databases such as UniProt and AGONOTES showed a much better performance on domain annotations, which is fundamental in studying the new Ago. AGONOTES can be freely accessed at http://i.uestc.edu.cn/agonotes/. AGONOTES is a friendly tool for annotating Ago domains from a proteome or a series of protein sequences.

中文翻译:

约定:Argonaute蛋白的机器人注释器。

几乎所有生物中都存在精氨酸蛋白(Ago)。在真核生物中,它充当基因表达的调节系统。在原核生物中,它是一种针对外来入侵基因组的防御系统。Ago系统已设计用于基因沉默和基因组编辑,并在生物学研究中发挥着重要作用。随着越来越多的各种微生物的基因组和蛋白质组变得可用,迫切需要用于识别和注释精氨酸蛋白的计算工具。我们介绍AGONOTES(Argonaute笔记)。这是专门为识别和注释Ago而设计的Web服务。AGONOTES使用BLASTP相似性搜索算法将所有提交的蛋白质分为三类:原核精子蛋白质(pAgo),真核精子蛋白质(eAgo)和非精子蛋白质(non-Ago)。然后可以使用多序列比对程序MUSCLE将Argonaute蛋白与相应的Ago序列标准组进行比对。Ago的所有功能域都可以从比对结果中进一步确定,并可以通过BioPerl套件中的Bio :: Graphic模块轻松查看。与现有的工具(如CD-Search)和可用的数据库(如UniProt和AGONOTES)相比,域标注的性能要好得多,这对于研究新的Ago至关重要。可以从http://i.uestc.edu.cn/agonotes/免费访问AGONOTES。AGONOTES是用于从蛋白质组或一系列蛋白质序列注释Ago域的友好工具。Ago的所有功能域都可以从比对结果中进一步确定,并可以通过BioPerl套件中的Bio :: Graphic模块轻松查看。与现有的工具(如CD-Search)和可用的数据库(如UniProt和AGONOTES)相比,域标注的性能要好得多,这对于研究新的Ago至关重要。可以在http://i.uestc.edu.cn/agonotes/上免费访问AGONOTES。AGONOTES是用于从蛋白质组或一系列蛋白质序列注释Ago域的友好工具。Ago的所有功能域都可以从比对结果中进一步确定,并可以通过BioPerl套件中的Bio :: Graphic模块轻松查看。与现有的工具(如CD-Search)和可用的数据库(如UniProt和AGONOTES)相比,域标注的性能要好得多,这对于研究新的Ago至关重要。可以从http://i.uestc.edu.cn/agonotes/免费访问AGONOTES。AGONOTES是用于从蛋白质组或一系列蛋白质序列注释Ago域的友好工具。可以从http://i.uestc.edu.cn/agonotes/免费访问AGONOTES。AGONOTES是用于从蛋白质组或一系列蛋白质序列注释Ago域的友好工具。可以从http://i.uestc.edu.cn/agonotes/免费访问AGONOTES。AGONOTES是用于从蛋白质组或一系列蛋白质序列注释Ago域的友好工具。
更新日期:2019-11-18
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