Secreted protein prediction system combining CJ-SPHMM, TMHMM, and PSORT

doi:10.1007/s00335-003-2296-6

CORC > 北京大学 > 生命科学学院

	Secreted protein prediction system combining CJ-SPHMM, TMHMM, and PSORT
	Chen, YJ ; Yu, P ; Luo, JC ; Jiang, Y
刊名	哺乳动物基因组
	2003
关键词	HIDDEN MARKOV MODEL SIGNAL PEPTIDE SUBCELLULAR-LOCALIZATION SORTING SIGNALS CLEAVAGE SITES SEQUENCE IDENTIFICATION GENOME GENERATION ALIGNMENT
DOI	10.1007/s00335-003-2296-6
英文摘要	To increase the coverage of secreted protein prediction, we describe a combination strategy. Instead of using a single method, we combine Hidden Markov Model (HMM)-based methods CJ-SPHMM and TMHMM with PSORT in secreted protein prediction. CJ-SPHMM is an HMM-based signal peptide prediction method, while TMHMM is an HMM-based transmembrane (TM) protein prediction algorithm. With CJ-SPHMM and TMHMM, proteins with predicted signal peptide and without predicted TM regions are taken as putative secreted proteins. This HMM-based approach predicts secreted protein with Ac (Accuracy) at 0.82 and Cc (Correlation coefficient) at 0.75, which are similar to PSORT with Ac at 0.82 and Cc at 0.76. When we further complement the HMM-based method, i.e., CJ-SPHMM + TMHMM with PSORT in secreted protein prediction, the Ac value is increased to 0.86 and the Cc value is increased to 0.81. Taking this combination strategy to search putative secreted proteins from the International Protein Index (IPI) maintained at the European Bioinformatics Institute (FBI), we constructed a putative human secretome with 5235 proteins. The prediction system described here can also be applied to predicting secreted proteins from other vertebrate proteomes.; Biochemistry & Molecular Biology; Biotechnology & Applied Microbiology; Genetics & Heredity; SCI(E); PubMed; 46; ARTICLE; 12; 859-865; 14
语种	英语
内容类型	期刊论文
源URL	[http://ir.pku.edu.cn/handle/20.500.11897/200018]
专题	生命科学学院
推荐引用方式 GB/T 7714	Chen, YJ,Yu, P,Luo, JC,et al. Secreted protein prediction system combining CJ-SPHMM, TMHMM, and PSORT[J]. 哺乳动物基因组,2003.
APA	Chen, YJ,Yu, P,Luo, JC,&Jiang, Y.(2003).Secreted protein prediction system combining CJ-SPHMM, TMHMM, and PSORT.哺乳动物基因组.
MLA	Chen, YJ,et al."Secreted protein prediction system combining CJ-SPHMM, TMHMM, and PSORT".哺乳动物基因组 (2003).