A novel approach for prediction of protein subcellular localization using optimal local information

Zhongshan Daxue Xuebao/Acta Scientiarum Natralium Universitatis Sunyatseni

Volumn 47, Issue 6, 2008, Pages 16-21

  Zhang, Shu Bo ^a   Lai, Jian Huang ^a   He, Jian Guo ^a  

^a SUN YAT SEN UNIVERSITY   (China)

Author keywords

Mature protein; N terminal sorting signal; Splice site; Subcellular localization; Support vector machine

Indexed keywords

EID: 61949441540     PISSN: 05296579     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (15)

1. HOGLUND A, DONNES P, BLUM T, et al. MultiLoc: Prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition [J]. Bioinformatics, 2006, 22 (10): 1158-1165.
2. PETSALAKI E I, BAGOS P G, LITOU Z I, et al. PredSL: A tool for the N-terminal sequence-based prediction of protein subcellular location [J]. Genomics Proteomics Bioinformatics, 2006, 4: 48-55.
3. REINHARDT A, HUBBARD T. Using neural networks for prediction of the subcellular location of proteins [J]. Nucleic Acids Res, 1998, 26 (9): 2230-2236.
4. HUA S J, SUN Z R. Support vector machine approach for protein subcellular location prediction [J]. Bioinformatics, 2001, 17: 721-728.
5. MATSUDA S, VERT J P, SAIGO H, et al. A novel representation of protein sequences for prediction of subcellular location using support vector machines [J]. Protein Sci, 2005, 14: 2804-2813.
6. GUO J, LIN Y, SUN Z. A novel method for protein subcellular localization: Combining residue-couple model and SVM [C]. Proceedings of the 3rd Asia-Pacific Bioinformatics Conference, Singapore, 2005, 117-129.
7. CHOU K C, CAI Y D. Using functional domain composition and support vector machines for prediction of protein subcellular location [J]. J Biol Chem, 2002, 277 (48): 45765-45769.
8. SCOTT M S, THOMAS D Y, HALLETT M T. Predicting subcellular localization via protein motif co-occurrence [J]. Genome Res, 2004, 14: 1957-1966.
9. XIE D, LI A, WANG M. LOCSVMPSI: A web server for subcellular localization of eukaryotic proteins using SVM and profile of PSI-BLAST [J]. Nucleic Acids Res, 2005, 33: 105-110.
10. TAMURA T, AKUTSU T. Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition [J]. BMC Bioinformatics, 2007, 8: 466.
11. CHOU K C, CAI Y D. Prediction of protein subcellular locations by GO-FunD-PseAA predictor [J]. Biochem Biophys Res Commun, 2004, 320 (4): 1236-1239.
12. CHOU K C, SHEN H B. Large-scale plant protein subcellular location prediction [J]. J Cell Biochem, 2007, 100 (3): 665-678.
13. CHOU K C. Prediction of protein subcellular locations by incorporating quasi-sequence-order effect [J]. Biochem Biophys Res Commun, 2000, 278 (2): 477-483.
14. SCOTT D E, MICHAEL N H, THOMAS I S. A mechanism of protein localization: The signal hypothesis and bacteria [J]. J Cell Biol, 1980, 86: 701-711.
15. EMANUELESSON O. Predicting protein subcellular localization from amino acid sequences information [J]. Briefings in Bioinformatics, 2002, 3: 361-376.