protodesigner:一个自动化的蛋白质拓扑方案生成器。

IF 2.9 3区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS
Petar Petrov, Valerio Izzi
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引用次数: 0

摘要

背景:氨基酸序列表征是几乎任何蛋白质分析的基本部分,创建简洁清晰的蛋白质拓扑方案在蛋白质组学研究中非常重要。尽管存在许多数据库和预测服务器,但是将来自各种资源(有时是竞争资源)的数据合并到一个准备发布的方案中是具有挑战性的。结果:在这里,我们展示了蛋白质拓扑设计R包(protodesigner),用于从数据库接入号、来自多个预测服务器的原始结果或手动准备的特征表自动生成蛋白质拓扑方案。该应用程序提供了一个图形用户界面,在R Shiny中实现,托管Pfam的域生成器的增强版本,用于渲染视觉上吸引人的方案。结论:protodesigner可以通过查询UniProt或NCBI GenPept数据库轻松快速地生成拓扑方案,并优雅地结合各种资源的特征。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
ProToDeviseR: an automated protein topology scheme generator.

Background: Amino acid sequence characterization is a fundamental part of virtually any protein analysis, and creating concise and clear protein topology schemes is of high importance in proteomics studies. Although numerous databases and prediction servers exist, it is challenging to incorporate data from various, and sometimes contending, resources into a publication-ready scheme.

Results: Here, we present the Protein Topology Deviser R package (ProToDeviseR) for the automatic generation of protein topology schemes from database accession numbers, raw results from multiple prediction servers, or a manually prepared table of features. The application offers a graphical user interface, implemented in R Shiny, hosting an enhanced version of Pfam's domains generator for the rendering of visually appealing schemes.

Conclusions: ProToDeviseR can easily and quickly generate topology schemes by interrogating UniProt or NCBI GenPept databases and elegantly combine features from various resources.

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来源期刊
BMC Bioinformatics
BMC Bioinformatics 生物-生化研究方法
CiteScore
5.70
自引率
3.30%
发文量
506
审稿时长
4.3 months
期刊介绍: BMC Bioinformatics is an open access, peer-reviewed journal that considers articles on all aspects of the development, testing and novel application of computational and statistical methods for the modeling and analysis of all kinds of biological data, as well as other areas of computational biology. BMC Bioinformatics is part of the BMC series which publishes subject-specific journals focused on the needs of individual research communities across all areas of biology and medicine. We offer an efficient, fair and friendly peer review service, and are committed to publishing all sound science, provided that there is some advance in knowledge presented by the work.
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