Gneg-mPLoc: a top-down strategy to enhance the quality of predicting subcellular localization of Gram-negative bacterial proteins. (English) Zbl 1406.92211
Summary: By incorporating the information of gene ontology, functional domain, and sequential evolution, a new predictor called Gneg-mPLoc was developed. It can be used to identify Gram-negative bacterial proteins among the following eight locations: (1) cytoplasm, (2) extracellular, (3) fimbrium, (4) flagellum, (5) inner membrane, (6) nucleoid, (7) outer membrane, and (8) periplasm. It can also be used to deal with the case when a query protein may simultaneously exist in more than one location. Compared with the original predictor called Gneg-PLoc, the new predictor is much more powerful and flexible. For a newly constructed stringent benchmark dataset in which none of proteins included has \(\geq 25\%\) pairwise sequence identity to any other in a same subset (location), the overall jackknife success rate achieved by Gneg-mPLoc was 85.5%, which was more than 14% higher than the corresponding rate by the Gneg-PLoc. As a user friendly web-server, Gneg-mPLoc is freely accessible at http://www.csbio.sjtu.edu.cn/bioinf/Gneg-multi/.
MSC:
| 92C40 | Biochemistry, molecular biology |
| 92C37 | Cell biology |
| 62P10 | Applications of statistics to biology and medical sciences; meta analysis |
Keywords:
multiplex protein; homology search; representative proteins; gene ontology; functional domain; sequential evolution; ensemble classifier; fusion approachReferences:
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