Amino acid classification based spectrum kernel fusion for protein subnuclear localization.

BMC Bioinformatics
Suyu Mei, Wang Fei

Abstract

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. In this paper, we only use the amino acid information of protein seque...Continue Reading

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Citations

Jun 17, 2011·Journal of Human Genetics·Chee-Seng KuAgus Salim
Feb 3, 2011·BMC Bioinformatics·Suyu MeiShuigeng Zhou
Dec 29, 2012·BMC Bioinformatics·Melissa PronoldShahab Asgharzadeh
Jan 21, 2011·PloS One·Dandan ZhangChunyu Liu
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Dec 26, 2015·International Journal of Molecular Sciences·Shunfang Wang, Shuhui Liu
Sep 25, 2012·Journal of Theoretical Biology·Yongcui WangXiangsun Zhang
Dec 2, 2011·Journal of Human Genetics·Shu-Mei TeoYudi Pawitan
Sep 12, 2015·BMC Medical Genomics·Salvatore MasecchiaGian Paolo Tonini
Mar 20, 2021·Scientific Reports·Pamela Xing Yi SohPeter Williamson

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Methods Mentioned

BETA
feature extraction
phylogenetic profile

Software Mentioned

SpectrumKernels
BLOSUM62
SpectrumKernel I
LIBSVM
PSI
SpectrumKernel Ensemble
Nuc
eMotif
Lei SVM Ensemble
SpectrumKernel

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