A novel method for similarity analysis and protein sub-cellular localization prediction

Bioinformatics

Volumn 26, Issue 21, 2010, Pages 2678-2683

  Liao, Bo ^a   Liao, Benyou ^a   Sun, Xingming ^a   Zeng, Qingguang ^a  

^a HUNAN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ALGORITHM; ARTICLE; CHEMISTRY; METHODOLOGY; PROTEIN DATABASE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

ALGORITHMS; DATABASES, PROTEIN; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN;

EID: 77958498251     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq521     Document Type: Article

References (28)

1. Al-Shahib,A. et al. (2005a) Feature selection and the class imbalance problem in predicting protein function from sequence. Appl. Bioinform., 4, 195-203.
2. Al-Shahib,A. et al. (2005b) FRANKSUM: new feature selection method for protein function prediction. Int. J. Neural Syst., 15, 250-275.
3. Bai,F.L. and Wang,T.M. (2005) A 2-D graphical representation of protein sequences based on nucleotide triplet codons. Chem. Phys. Lett., 413, 458-462.
4. Bulashevska,A. and Eils,R. (2006) Predicting protein sub cellular locations using hierarchical ensemble of Bayesian classifiers based on Markov chains. BMC Bioinformatics, 7, 298.
5. Chen,Y.L. and Li,Q.Z. (2007a) Prediction of apoptosis protein sub cellular location using improved hybrid approach and pseudo-amino acid composition. J. Theor. Biol., 248, 377-381.
6. Chen,Y.L. and Li,Q.Z. (2007b) Prediction of the sub cellular location of apoptosis proteins. J. Theor. Biol., 245, 775-783.
7. Cao,Z. et al. (2008) A group of 3D graphical representation of DNA sequences based on dual nucleotides. Int. J. Quantum Chem., 108, 1485-1490.
8. Gao,Q.B. et al. (2005) Prediction of protein sub cellular location using a combined feature of sequence. Fed. Eur. Biochem. Soc., 579, 3444-3448.
9. He,P.A. et al. (2010) The graphical representation of protein sequences based on the physicochemical properties and its applications. J. Comput. Chem., 31, 2136-2142.
10. Liao,B. et al. (2005) A 4D representation of DNA sequences and its application. Chem. Phys. Lett., 402, 380-383.
11. Liao,B. and Zhu,W. (2006) Analysis of similarity/dissimilarity of DNA primary sequences based on condensed matrices and information entropies. Curr. Comput. Aid. Drug Des., 2, 275-285.
12. Liao,B. et al. (2007) On the similarity of DNA primary sequences based on 5D representation. J. Math. Chem., 42, 47-57.
13. Lee,R.B. et al. (2009) Identification of protein functions using a machine-learning approach based on sequence-derived properties. Proteome Sci., 7, 27.
14. Li,X. et al. (2009) Protein functional class prediction using global encoding of amino acid sequence. J. Theo. Biol., 261, 290-293.
15. Liu,Z.B. et al. (2009) A 2-D graphical representation of DNA sequence based on dual nucleotides and its application. Int. J. Quant. Chem., 109, 948-958.
16. Nandy,A. (1996) Two-dimensional graphical representation of DNA sequences and intron-exon discrimination in intron-rich sequences. Comput. Appl. Biosci., 12, 55-62.
17. Randić,M. (2000a) Condensed Representation of DNA Primary Sequences. J. Chem. Inform. Comput. Sci., 40, 50-56.
18. Randić,M. et al. (2000b) On 3-D graphical representation of DNA primary sequences and their numerical characterization. J. Chem. Inform. Comput. Sci., 40, 1235-1244.
19. Randić,M. et al. (2003a) Novel 2-D graphical representation of DNA sequences and their numerical characterization. Chem. Phys. Lett., 368, 1-6.
20. Randić,M. et al. (2003b) Analysis of similarity/dissimilarity Of DNA sequences based on novel 2-D graphical representation. Chem. Phys. Lett., 371, 202-207.
21. Randić,M. et al. (2004) Unique graphical representation of protein sequences based on nucleotide triplet codons. Chem. Phys. Lett., 397, 247-252.
22. Randić,M. (2007) 2-D Graphical representation of proteins based on physico-chemical properties of amino acids. Chem. Phys. Lett., 440, 291-295.
23. Randić,M. et al. (2009) Graphical representation of proteins as four-color maps and their numerical characterization. J. Mol. Graph. Model., 27, 637-641.
24. Wen,J. and Zhang,Y.Y. (2009) A 2D graphical representation of protein sequence and its numerical characterization. Chem. Phys. Lett., 476, 281-286.
25. Yu,J.F. et al. (2009)TN curve: A novel 3D graphical representation of DNA sequence based on trinucleotides and its applications. J. Theor. Biol., 261, 459-468.
26. Yu,J.F. and Sun,X. (2010) Reannotation of protein-coding genes based on an improved graphical representation of DNA sequence. J. Comput. Chem., 31, 2126-2135.
27. Zhou,G P. and Doctor,K. (2003) Sub cellular location prediction of apoptosis proteins. Proteins, 50, 44-48.
28. Zhang,L. et al. (2009) A novel representation for apoptosis protein subcellular localization prediction using support vector machine. J. Theor. Biol., 259, 361-365.