In silico identification of Gram-negative bacterial secreted proteins from primary sequence.
In this study, we focus on different types of Gram-negative bacterial secreted proteins, and try to analyze the relationships and differences among them. Through an extensive literature search, 1612 secreted proteins have been collected as a standard data set from three data sources, including Swiss-Prot, TrEMBL and RefSeq. To explore the relationships among different types of secreted proteins, we model this data set as a sequence similarity network. Finally, a multi-classifier named SecretP is proposed to distinguish different types of secreted proteins, and yields a high total sensitivity of 90.12% for the test set. When performed on another public independent dataset for further evaluation, a promising prediction result is obtained. Predictions can be implemented freely online at http://cic.scu.edu.cn/bioinformatics/secretPv2_1/index.htm.
College of Chemistry, Sichuan University, Chengdu 610064, PR China.
Lezheng
L
Yu
Jiesi
J
Luo
Yanzhi
Y
Guo
Yizhou
Y
Li
Xuemei
X
Pu
Menglong
M
Li
D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism*; D006090:Gram-Negative Bacteria / Q000235:genetics* / Q000378:metabolism*; D012680:Sensitivity and Specificity; D020539:Sequence Analysis, Protein / Q000295:instrumentation / Q000379:methods*
D001426:Bacterial Proteins
Multi-classifier; Pseudo-amino acid composition; Sequence similarity network; Support vector machine