LOCSVMPSI: a web server for subcellular localization of eukaryotic proteins using SVM and profile of PSI-BLAST.
LOCSVMPSI: a web server for subcellular localization of eukaryotic proteins using SVM and profile of PSI-BLAST.
复制标题
DOI：
10.1093/nar/gki359
复制
发表时间：
2005-07-01
影响因子：
14.9
通讯作者：
Feng H
中科院分区：
文献类型：
--
作者：
Xie D;Li A;Wang M;Fan Z;Feng H
蛋白质的亚细胞定位是关键的功能特征之一，因为蛋白质必须在亚细胞水平上正确定位才能具有正常的生物学功能。本文介绍了一种名为 LOCSVMPSI 的新方法，该方法基于支持向量机（SVM）和从 PSI-BLAST 的配置文件生成的特定位置评分矩阵。通过在RH2427数据集上的折刀测试，LOCSVMPSI取得了90.2%的较高整体预测精度，高于SubLoc和ESLpred在此数据集上的预测结果。此外，在 PK7579 数据集上通过 5 倍交叉验证测试评估了 LOCSVMPSI 的预测性能，预测结果始终优于之前基于使用氨基酸和氨基酸对组成的多个 SVM 的方法。在 SWISSPROT 新独特的数据集上的进一步测试表明，LOCSVMPSI 也比一些广泛使用的预测方法（例如 PSORTII、TargetP 和 LOCnet）表现更好。所有这些结果表明LOCSVMPSI是预测真核蛋白质亚细胞定位的有力工具。基于该方法的在线Web服务器（当前版本为1.3）已经开发出来，并且免费提供给学术和商业用户，可以通过以下网址访问。
Subcellular location of a protein is one of the key functional characters as proteins must be localized correctly at the subcellular level to have normal biological function. In this paper, a novel method named LOCSVMPSI has been introduced, which is based on the support vector machine (SVM) and the position-specific scoring matrix generated from profiles of PSI-BLAST. With a jackknife test on the RH2427 data set, LOCSVMPSI achieved a high overall prediction accuracy of 90.2%, which is higher than the prediction results by SubLoc and ESLpred on this data set. In addition, prediction performance of LOCSVMPSI was evaluated with 5-fold cross validation test on the PK7579 data set and the prediction results were consistently better than the previous method based on several SVMs using composition of both amino acids and amino acid pairs. Further test on the SWISSPROT new-unique data set showed that LOCSVMPSI also performed better than some widely used prediction methods, such as PSORTII, TargetP and LOCnet. All these results indicate that LOCSVMPSI is a powerful tool for the prediction of eukaryotic protein subcellular localization. An online web server (current version is 1.3) based on this method has been developed and is freely available to both academic and commercial users, which can be accessed by at .
登录
查看更多内容
影响因子：
8
作者：
Ouali, M;King, RD
通讯作者：
King, RD
影响因子：
14.9
作者：
Reinhardt, A;Hubbard, T
通讯作者：
Hubbard, T
影响因子：
5.6
作者：
Jones, DT
通讯作者：
Jones, DT
DOI：
10.1016/j.bbrc.2004.08.113
发表时间：
2004-10-15
影响因子：
3.1
作者：
Cai, YD;Chou, KC
通讯作者：
Chou, KC
影响因子：
5.8
作者：
Gardy, JL;Laird, MR;Brinkman, FSL
通讯作者：
Brinkman, FSL