title: Secreted protein prediction system combining CJ-SPHMM, TMHMM, and PSORT.
abstract: 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 (EBI), 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.
authors.affiliation: College of Life Sciences, National Laboratory of Protein Engineering and Plant Genetic Engineering, and Centre of Bioinformatics, Peking University, Beijing 100871, China.
authors.forename: Yunjia
authors.initials: Y
authors.lastname: Chen
authors.forename: Peng
authors.initials: P
authors.lastname: Yu
authors.forename: Jingchu
authors.initials: J
authors.lastname: Luo
authors.forename: Ying
authors.initials: Y
authors.lastname: Jiang
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D006801:Humans; D008565:Membrane Proteins / Q000235:genetics*; D021382:Protein Sorting Signals / Q000235:genetics*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D020539:Sequence Analysis, Protein
chemical_list: D008565:Membrane Proteins; D021382:Protein Sorting Signals