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

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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.

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Acknowledgements

This work was supported by China High-Tech Program (grant No 2001AA231011) and the Beijing Municipal Committee of Science and Technology (grant No H010210360119). We thank Dr. Kenta Nakai and Dr. Anders Krogh for their kindness in providing us PSORT and TMHMM running on our server locally. We also thank Mr. Yanbin Yin for some valuable suggestion.

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  1. College of Life Sciences, National Laboratory of Protein Engineering and Plant Genetic Engineering, and Centre of Bioinformatics, Peking University, Beijing 100871, China

    Yunjia Chen, Peng Yu, Jingchu Luo & Ying Jiang

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  1. Yunjia Chen
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  2. Peng Yu
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  3. Jingchu Luo
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  4. Ying Jiang
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Correspondence to Ying Jiang.

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Chen, Y., Yu, P., Luo, J. et al. Secreted protein prediction system combining CJ-SPHMM, TMHMM, and PSORT . Mamm Genome 14, 859–865 (2003). https://doi.org/10.1007/s00335-003-2296-6

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  • DOI: https://doi.org/10.1007/s00335-003-2296-6

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