细菌细胞表面蛋白质组注释的生物信息学工作流。

Q2 Decision Sciences
Andrew J Perry, Bosco K Ho
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引用次数: 14

摘要

背景:表面暴露细菌膜蛋白的注释是蛋白质组学实验解释和验证的重要步骤。特别是,通过细胞表面蛋白酶刮除实验检测到的蛋白质可以指出膜蛋白的暴露区域,这些区域可能含有抗原决定因子或构成致病菌的疫苗靶点。结果:Inmembrane是一种预测细菌蛋白质序列中多肽表面暴露区域膜蛋白的工具。我们重新实施了革兰氏阳性细菌蛋白质组的方案,并开发了革兰氏阴性细菌的新方案,该方案与亚细胞定位和膜蛋白拓扑的多种预测因子相结合。通过使用现代脚本语言,inmembrane提供了一个可访问的代码库和可扩展的体系结构,可以修改相关的序列注释任务。结论:Inmembrane很容易集成来自本地二进制和基于web的查询的预测,以帮助获得细菌蛋白质组中可能表面暴露的蛋白质的概述。该程序托管在Github存储库http://github.com/boscoh/inmembrane上。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Inmembrane, a bioinformatic workflow for annotation of bacterial cell-surface proteomes.

Inmembrane, a bioinformatic workflow for annotation of bacterial cell-surface proteomes.

Inmembrane, a bioinformatic workflow for annotation of bacterial cell-surface proteomes.

Inmembrane, a bioinformatic workflow for annotation of bacterial cell-surface proteomes.

Background: The annotation of surface exposed bacterial membrane proteins is an important step in interpretation and validation of proteomic experiments. In particular, proteins detected by cell surface protease shaving experiments can indicate exposed regions of membrane proteins that may contain antigenic determinants or constitute vaccine targets in pathogenic bacteria.

Results: Inmembrane is a tool to predict the membrane proteins with surface-exposed regions of polypeptide in sets of bacterial protein sequences. We have re-implemented a protocol for Gram-positive bacterial proteomes, and developed a new protocol for Gram-negative bacteria, which interface with multiple predictors of subcellular localization and membrane protein topology. Through the use of a modern scripting language, inmembrane provides an accessible code-base and extensible architecture that is amenable to modification for related sequence annotation tasks.

Conclusions: Inmembrane easily integrates predictions from both local binaries and web-based queries to help gain an overview of likely surface exposed protein in a bacterial proteome. The program is hosted on the Github repository http://github.com/boscoh/inmembrane.

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来源期刊
Source Code for Biology and Medicine
Source Code for Biology and Medicine Decision Sciences-Information Systems and Management
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期刊介绍: Source Code for Biology and Medicine is a peer-reviewed open access, online journal that publishes articles on source code employed over a wide range of applications in biology and medicine. The journal"s aim is to publish source code for distribution and use in the public domain in order to advance biological and medical research. Through this dissemination, it may be possible to shorten the time required for solving certain computational problems for which there is limited source code availability or resources.
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