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Searching algorithm for type IV secretion system effectors 1.0: a tool for predicting type IV effectors and exploring their genomic context

机译:IV型分泌系统效应子1.0的搜索算法:一种预测IV型效应子并探索其基因组背景的工具

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摘要

Type IV effectors (T4Es) are proteins produced by pathogenic bacteria to manipulate host cell gene expression and processes, divert the cell machinery for their own profit and circumvent the immune responses. T4Es have been characterized for some bacteria but many remain to be discovered. To help biologists identify putative T4Es from the complete genome of α- and γ-proteobacteria, we developed a Perl-based command line bioinformatics tool called S4TE (searching algorithm for type-IV secretion system effectors). The tool predicts and ranks T4E candidates by using a combination of 13 sequence characteristics, including homology to known effectors, homology to eukaryotic domains, presence of subcellular localization signals or secretion signals, etc. S4TE software is modular, and specific motif searches are run independently before ultimate combination of the outputs to generate a score and sort the strongest T4Es candidates. The user keeps the possibility to adjust various searching parameters such as the weight of each module, the selection threshold or the input databases. The algorithm also provides a GC% and local gene density analysis, which strengthen the selection of T4E candidates. S4TE is a unique predicting tool for T4Es, finding its utility upstream from experimental biology.
机译:IV型效应子(T4Es)是由病原菌产生的蛋白质,可操纵宿主细胞的基因表达和过程,转移细胞机制以牟利,并规避免疫反应。 T4Es已针对某些细菌进行了表征,但仍有许多待发现。为帮助生物学家从α-和γ-变形杆菌的完整基因组中鉴定出假定的T4E,我们开发了一种基于Perl的命令行生物信息学工具,称为S4TE(用于IV型分泌系统效应子的搜索算法)。该工具通过使用13种序列特征的组合来预测T4E候选者并对其进行排名,包括与已知效应子的同源性,与真核域的同源性,亚细胞定位信号或分泌信号的存在等。S4TE软件是模块化的,并且特定基序搜索可独立运行最后将输出进行最终组合以生成分数并对最强的T4E候选者进行排序。用户可以调整各种搜索参数,例如每个模块的重量,选择阈值或输入数据库。该算法还提供了GC%和局部基因密度分析,从而加强了对T4E候选基因的选择。 S4TE是T4E的独特预测工具,在实验生物学的上游发现了它的效用。

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