Predicting apoptosis protein subcellular localization by integrating auto-cross correlation and PSSM into Chou’s PseAAC. (English) Zbl 1406.92230
Summary: The prediction of subcellular localization of an apoptosis protein is still a challenging task, and existing methods mainly based on protein primary sequences. In this study, we propose a novel model called MACC-PSSM by integrating Moran autocorrelation and cross correlation with PSSM. Then a 3600-dimensional feature vector is constructed to predict apoptosis protein subcellular localization. Finally, 210 features are selected using principal component analysis (PCA) on the ZW225 dataset, and support vector machine is adopted as classifier. To evaluate the performance of the proposed method, jackknife cross-validation tests are performed on two widely used benchmark datasets: ZW225 and CL317. Our model achieves competitive performance on prediction accuracies, especially for the overall prediction accuracies for datasets ZW225 and CL317, which reach 84.9% and 90.5%, respectively. Comparison of our results with other methods demonstrates that MACC-PSSM model can be used as a potential candidate for the accurate prediction of apoptosis protein subcellular localization.
MSC:
| 92C40 | Biochemistry, molecular biology |
| 92C37 | Cell biology |
| 92D20 | Protein sequences, DNA sequences |
| 68T05 | Learning and adaptive systems in artificial intelligence |
| 62P10 | Applications of statistics to biology and medical sciences; meta analysis |
Keywords:
protein subcellular localization; autocorrelation function; cross correlation; support vector machine; PSSMSoftware:
LIBSVM; iPromoter-2L; PSI-BLAST; pSuc-Lys; iRSpot-EL; iLoc-Euk; iRSpot-PseDNC; iEnhancer-EL; iPTM-mLys; iRNA-PseColl; iRSpot-Pse6NC; iHSP-PseRAAAC; iLoc-lncRNA; iRNA-3typeA; iPro54-PseKNC; iDNA6mA-PseKNC; 2L-piRNA; pLoc_bal-mGpos; iSS-PseDNC; iRO-3wPseKNC; iOri-Human; iNitro-Tyr; pLoc-mHum; pLoc-mGneg; Pse-in-One; PseKNC; pLoc-mPlant; iACP; pLoc-mEuk; pLoc-mVirus; pLoc-mAnimal; BLAST; iRNA-AI; PISCESReferences:
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