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亚细胞定位工具汇总

2021/7/12

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亚细胞定位是指某种蛋白或某个基因表达产物在细胞内的具体存在部位，包括细胞核、细胞质和细胞膜以及各种细胞器等。

下面是一篇文章对各种工具做了汇总和比较：

A list of published protein subcellular localization prediction toolsTool NameLocations or Protein Features PredictedOrganism CategoriesPublication Reference TargetP extracellular, mitochondrial, chloroplastnon-plant, plant Emanuelsson, O., Nielsen, H., Brunak, S., & von Heijne, G. (2000) Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. Journal of molecular biology, 300(4), 1005-1016. TMHMM transmembrane helicesany Krogh, A., Larsson, B., von Heijne, G., & Sonnhammer, E. L. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. Journal of molecular biology, 305(3), 567-580. scanProsite (PS-Scan) ER retention signalany de Castro E, Sigrist CJ, Gattiker A, Bulliard V, Langendijk-Genevaux PS, Gasteiger E, Bairoch A, Hulo N. (2006) ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Res., 34(Web Server issue), W362-365. SecretomeP 2.0 non-classical i.e. not signal peptide triggered protein secretiongram-positive bacteria, gram-negative bacteria, mammal Bendtsen J.D., Jensen,L.J., Blom,N., et al. (2004) Feature based prediction of non-classical and leaderless protein secretion. Protein Eng. Des. Sel., 17, 349-356. Phobius signal peptide and transmembrane topologyany Käll, L., Krogh, A., & Sonnhammer, E. L. L. (2007) Advantages of combined transmembrane topology and signal peptide prediction–the Phobius web server.. Nucleic Acids Res., 35(Web Server issue), W429-432. WoLF PSORT > 5 locationsfungi, plant, animal Horton, P., Park, K.-J., Obayashi, T., Fujita, N., Harada, H., Adams-Collier, C. J., & Nakai, K. (2007) WoLF PSORT: protein localization predictor. Nucleic Acids Res., 35(Web Server issue), W585-587. PRED-LIPO lipoprotein signal peptidesgram-positive bacteria Bagos, Pantelis G, Tsirigos, K. D., Liakopoulos, T. D., & Hamodrakas, S. J. (2008) Prediction of lipoprotein signal peptides in Gram-positive bacteria with a Hidden Markov Model. Journal of proteome research, 7(12), 5082-5093. ProLoc-GO > 5 locationshuman and eukaryotes Huang, W.-L., Tung, C.-W., Ho, S.-W., Hwang, S.-F., & Ho, S.-Y. (2008) ProLoc-GO: utilizing informative Gene Ontology terms for sequence-based prediction of protein subcellular localization. BMC bioinformatics, 9, 80. KnowPredsite > 5 locationsprokaryotes and eukaryotes Lin, H.-N., Chen, C.-T., Sung, T.-Y., Ho, S.-Y., & Hsu, W.-L. (2009) Protein subcellular localization prediction of eukaryotes using a knowledge-based approach. BMC bioinformatics, 10 Suppl 15, S8. MultiLoc2 > 5 locationsanimal, fungal, plant Blum, T, Briesemeister, S, and Kohlbacher, O (2009) MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction. BMC Bioinformatics, 10:274. PRED-SIGNAL signal peptidesarchaea Bagos, P G, Tsirigos, K. D., Plessas, S. K., Liakopoulos, T. D., & Hamodrakas, S. J. (2009) Prediction of signal peptides in archaea. Protein engineering, design & selection: PEDS, 22(1), 27-35. RSLPred chloroplast, cytoplasm, mitochondria, nucleusoryza sativa only Kaundal, R., & Raghava, G. P. S. (2009) RSLpred: an integrative system for predicting subcellular localization of rice proteins combining compositional and evolutionary information. Proteomics, 9(9), 2324-2342. SherLoc2 > 5 locationsanimal, fungi, plant Briesemeister, S., Blum, T., Brady, S., Lam, Y., Kohlbacher, O., & Shatkay, H. (2009) SherLoc2: a high-accuracy hybrid method for predicting subcellular localization of proteins. Journal of proteome research, 8(11), 5363-5366. Cell-PLoc 2.0 > 5 locationseukaryote, human, plant, virus, gram-positive bacteria, gram-negative bacteria Chou, K. and Shen, H. (2010) Cell-PLoc 2.0: an improved package of web-servers for predicting subcellular localization of proteins in various organisms. Natural Science, 2, 1090-1103. CoBaltDB > 5 locationsprokaryotes Goudenège, D., Avner, S., Lucchetti-Miganeh, C., & Barloy-Hubler, F. (2010) CoBaltDB: Complete bacterial and archaeal orfeomes subcellular localization database and associated resources. BMC microbiology, 10, 88. PSORTb > 5 locationsgram-positive and gram-negative bacteria Yu, N. Y., Wagner, J. R., Laird, M. R., Melli, G., Rey, S., Lo, R., … Brinkman, F. S. L. (2010) PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics (Oxford, England), 26(13), 1608-1615. SCLPred cytoplasm, mitochondrion, nucleus, secretory, chloroplastanimals, plants, fungi Mooney, C., Wang, Y.-H., & Pollastri, G. (2011) SCLpred: protein subcellular localization prediction by N-to-1 neural networks. Bioinformatics (Oxford, England), 27(20), 2812-2819. SignalP 4.0 signal peptideeukaryotic, gram-positive bacteria, gram-negative bacteria Petersen, T. N., Brunak, S., von Heijne, G., & Nielsen, H. (2011) SignalP 4.0: discriminating signal peptides from transmembrane regions. Nature methods, 8(10), 785-786. SlocX > 5 locationsaribdopsis thaliana only Ryngajllo, M., Childs, L., Lohse, M., Giorgi, F. M., Lude, A., Selbig, J., & Usadel, B. (2011) SLocX: Predicting Subcellular Localization of Arabidopsis Proteins Leveraging Gene Expression Data. Frontiers in plant science, 2, 43. APSLAP > 5 locationsapoptosis Saravanan, V., & Lakshmi, P. T. V. (2013) APSLAP: An Adaptive Boosting Technique for Predicting Subcellular Localization of Apoptosis Protein. Acta biotheoretica, . Iloc Animal > 5 locationsanimal Lin, W.-Z., Fang, J.-A., Xiao, X., & Chou, K.-C. (2013) iLoc-Animal: a multi-label learning classifier for predicting subcellular localization of animal proteins. Molecular bioSystems, 9(4), 634-644.

参考资料：

1. Meinken J, Min XJ. (2012) Computational prediction of protein subcellular locations in eukaryotes: an experience report. Computational Molecular Biology. 2(1): 1-7 (doi: 10.5376/cmb.2012.02.0001).

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作者：陈浩

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数据分析工具

Cell-PLoc 2.0, CoBaltDB, KnowPredsite, MultiLoc2, Phobius, PRED-LIPO, PRED-SIGNAL, ProLoc-GO, RSLPred, scanProsite (PS-Scan), SecretomeP, SherLoc2, SignalP, TargetP, TMHMM, WoLF PSORT, 亚细胞定位

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