GNBSL: a new integrative system to predict the subcellular location for Gram-negative bacteria proteins.
This paper proposes a new integrative system (GNBSL--Gram-negative bacteria subcellular localization) for subcellular localization specifized on the Gram-negative bacteria proteins. First, the system generates a position-specific frequency matrix (PSFM) and a position-specific scoring matrix (PSSM) for each protein sequence by searching the Swiss-Prot database. Then different features are extracted by four modules from the PSFM and the PSSM. The features include whole-sequence amino acid composition, N- and C-terminus amino acid composition, dipeptide composition, and segment composition. Four probabilistic neural network (PNN) classifiers are used to classify these modules. To further improve the performance, two modules trained by support vector machine (SVM) are added in this system. One module extracts the residue-couple distribution from the amino acid sequence and the other module applies a pairwise profile alignment kernel to measure the local similarity between every two sequences. Finally, an additional SVM is used to fuse the outputs from the six modules. Test on a benchmark dataset shows that the overall success rate of GNBSL is higher than those of PSORT-B, CELLO, and PSLpred. A web server GNBSL can be visited from http://166.111.24.5/webtools/GNBSL/index.htm.
Guo
Jian
J
Department of Mathematical Sciences, Laboratory of Statistical Computing & Bioinformatics, Tsinghua University, Beijing, P R China. genovo@126.com
Lin
Yuanlie
Y
Liu
Xiangjun
X
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000378:metabolism*; D019295:Computational Biology; D006090:Gram-Negative Bacteria / Q000166:cytology / Q000378:metabolism*; D008969:Molecular Sequence Data; D011237:Predictive Value of Tests; D012984:Software; D013347:Subcellular Fractions / Q000378:metabolism
D001426:Bacterial Proteins