Amino acid classification based spectrum kernel fusion for protein subnuclear localization

BMC Bioinformatics. 2010 Jan 18;11 Suppl 1(Suppl 1):S17. doi: 10.1186/1471-2105-11-S1-S17.


Background: Prediction of protein localization in subnuclear organelles is more challenging than general protein subcelluar localization. There are only three computational models for protein subnuclear localization thus far, to the best of our knowledge. Two models were based on protein primary sequence only. The first model assumed homogeneous amino acid substitution pattern across all protein sequence residue sites and used BLOSUM62 to encode k-mer of protein sequence. Ensemble of SVM based on different k-mers drew the final conclusion, achieving 50% overall accuracy. The simplified assumption did not exploit protein sequence profile and ignored the fact of heterogeneous amino acid substitution patterns across sites. The second model derived the PsePSSM feature representation from protein sequence by simply averaging the profile PSSM and combined the PseAA feature representation to construct a kNN ensemble classifier Nuc-PLoc, achieving 67.4% overall accuracy. The two models based on protein primary sequence only both achieved relatively poor predictive performance. The third model required that GO annotations be available, thus restricting the model's applicability.

Methods: In this paper, we only use the amino acid information of protein sequence without any other information to design a widely-applicable model for protein subnuclear localization. We use K-spectrum kernel to exploit the contextual information around an amino acid and the conserved motif information. Besides expanding window size, we adopt various amino acid classification approaches to capture diverse aspects of amino acid physiochemical properties. Each amino acid classification generates a series of spectrum kernels based on different window size. Thus, (I) window expansion can capture more contextual information and cover size-varying motifs; (II) various amino acid classifications can exploit multi-aspect biological information from the protein sequence. Finally, we combine all the spectrum kernels by simple addition into one single kernel called SpectrumKernel+ for protein subnuclear localization.

Results: We conduct the performance evaluation experiments on two benchmark datasets: Lei and Nuc-PLoc. Experimental results show that SpectrumKernel+ achieves substantial performance improvement against the previous model Nuc-PLoc, with overall accuracy 83.47% against 67.4%; and 71.23% against 50% of Lei SVM Ensemble, against 66.50% of Lei GO SVM Ensemble.

Conclusion: The method SpectrumKernel+ can exploit rich amino acid information of protein sequence by embedding into implicit size-varying motifs the multi-aspect amino acid physiochemical properties captured by amino acid classification approaches. The kernels derived from diverse amino acid classification approaches and different sizes of k-mer are summed together for data integration. Experiments show that the method SpectrumKernel+ significantly outperforms the existing models for protein subnuclear localization.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Amino Acids / classification*
  • Databases, Protein
  • Protein Conformation
  • Proteins / analysis*
  • Proteins / classification
  • Proteomics / methods*
  • Sequence Analysis, Protein


  • Amino Acids
  • Proteins