PSORTb v.2.0: Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis
PSORTb v.2.0: Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis
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DOI：
10.1093/bioinformatics/bti057
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发表时间：
2005-03-01
期刊：
影响因子：
5.8
通讯作者：
Brinkman, FSL
中科院分区：
文献类型：
--
作者：
Gardy, JL;Laird, MR;Brinkman, FSL
动机：PSORTb v.1.1是目前最精确的细菌定位预测工具。然而，该程序的预测覆盖率和召回率较低，并且该方法仅适用于革兰氏阴性菌。目前工作的目标如下：增加PSORTb的覆盖面，同时保持现有的精度水平，扩大它包括革兰氏阳性菌，然后进行localization.Results的比较分析：一个扩展的数据库的蛋白质的已知定位和新的模块，使用频繁的基于重复性的支持向量机被引入到PSORTb V.2.0。该程序对革兰氏阳性菌和革兰氏阴性菌的精确度达到96%，预测覆盖率与其他全蛋白质组分析工具相当。我们发现，蛋白质在每个位置的比例是非常一致的物种，即使在不同的蛋白质组大小的物种。
Motivation: PSORTb v.1.1 is the most precise bacterial localization prediction tool available. However, the program's predictive coverage and recall are low and the method is only applicable to Gram-negative bacteria. The goals of the present work are as follows: increase PSORTb's coverage while maintaining the existing precision level, expand it to include Gram-positive bacteria and then carry out a comparative analysis of localization.Results: An expanded database of proteins of known localization and new modules using frequent subsequence-based support vector machines was introduced into PSORTb v.2.0. The program attains a precision of 96% for Gram-positive and Gram-negative bacteria and predictive coverage comparable to other tools for whole proteome analysis. We show that the proportion of proteins at each localization is remarkably consistent across species, even in species with varying proteome size.