Gardy J L, Laird M R, Chen F, Rey S, Walsh C J, Ester M, Brinkman F S L
Department of Molecular Biology and Biochemistry, Simon Fraser University Burnaby, BC, Canada V5A 1S6.
Bioinformatics. 2005 Mar 1;21(5):617-23. doi: 10.1093/bioinformatics/bti057. Epub 2004 Oct 22.
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.
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.
Web-based version: http://www.psort.org/psortb. Standalone version: Available through the website under GNU General Public License.
psort-mail@sfu.ca, brinkman@sfu.ca
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，且该方法仅适用于革兰氏阴性菌。本研究的目标如下：在保持现有精度水平的同时提高PSORTb的覆盖率，将其扩展至包括革兰氏阳性菌，然后进行定位的比较分析。
PSORTb v.2.0引入了一个扩展的已知定位蛋白质数据库以及使用基于频繁子序列的支持向量机的新模块。该程序对革兰氏阳性菌和革兰氏阴性菌的预测精度达到96%，且预测覆盖率与其他用于全蛋白质组分析的工具相当。我们发现，即使在蛋白质组大小不同的物种中，每个定位的蛋白质比例在不同物种间也非常一致。
基于网络的版本：http://www.psort.org/psortb。独立版本：可通过该网站根据GNU通用公共许可证获取。
psort-mail@sfu.ca，brinkman@sfu.ca
