pLoc-mGneg: Predict subcellular localization of Gram-negative bacterial proteins by deep gene ontology learning via general PseAAC

• Published in: Genomics (San Diego, Calif.) Calif.), 2018-07, Vol.110 (4), p.231-239
• Main Authors: Cheng, Xiang, Xiao, Xuan, Chou, Kuo-Chen
• Format: Article
• Language: English
• Subjects: Chou's general PseAAC; Chou's metrics; Gene ontology; ML-GKR; Multi-label system
• ISSN: 0888-7543; 1089-8646
• DOI: 10.1016/j.ygeno.2017.10.002

Information of the proteins' subcellular localization is crucially important for revealing their biological functions in a cell, the basic unit of life. With the avalanche of protein sequences generated in the postgenomic age, it is highly desired to develop computational tools for timely identifying their subcellular locations based on the sequence information alone. The current study is focused on the Gram-negative bacterial proteins. Although considerable efforts have been made in protein subcellular prediction, the problem is far from being solved yet. This is because mounting evidences have indicated that many Gram-negative bacterial proteins exist in two or more location sites. Unfortunately, most existing methods can be used to deal with single-location proteins only. Actually, proteins with multi-locations may have some special biological functions important for both basic research and drug design. In this study, by using the multi-label theory, we developed a new predictor called “pLoc-mGneg” for predicting the subcellular localization of Gram-negative bacterial proteins with both single and multiple locations. Rigorous cross-validation on a high quality benchmark dataset indicated that the proposed predictor is remarkably superior to “iLoc-Gneg”, the state-of-the-art predictor for the same purpose. For the convenience of most experimental scientists, a user-friendly web-server for the novel predictor has been established at http://www.jci-bioinfo.cn/pLoc-mGneg/, by which users can easily get their desired results without the need to go through the complicated mathematics involved. •We proposed a new predictor for predicting the subcellular localization of bacteria Gram-negative proteins with both single and multiple location sites.•It represents a revolutionary breakthrough in this area since its success rates are overwhelmingly better than those of the existing state-of-the-art methods.•Its web-server has been established by which users can easily get their desired results.