Amino acid classification based spectrum kernel fusion for protein subnuclear localization

BMC Bioinformatics

Volumn 11, Issue SUPPLL.1, 2010, Pages

  Mei, Suyu ^a   Fei, Wang ^a  

^a FUDAN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SUBSTITUTION; BIOLOGICAL INFORMATION; CLASSIFICATION APPROACH; CONTEXTUAL INFORMATION; PHYSIO-CHEMICAL PROPERTIES; PREDICTIVE PERFORMANCE; PROTEIN SEQUENCE PROFILES; SUBNUCLEAR LOCALIZATION;

AMINO ACIDS; EXPERIMENTS;

PROTEINS;

AMINO ACID; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CLASSIFICATION; METHODOLOGY; PROTEIN CONFORMATION; PROTEIN DATABASE; PROTEOMICS; SEQUENCE ANALYSIS;

AMINO ACID SEQUENCE; AMINO ACIDS; DATABASES, PROTEIN; PROTEIN CONFORMATION; PROTEINS; PROTEOMICS; SEQUENCE ANALYSIS, PROTEIN;

EID: 75149113268     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-S1-S17     Document Type: Article

References (31)

1. Lei Z, Dai Y. An SVM-based system for predicting protein subnuclear localizations. BMC Bioinformatics 2005, 6:291. 10.1186/1471-2105-6-291, 1325059, 16336650.
2. Shen H, Chou K. Nuc-PLoc: a new web-server for predicting protein subnuclear localization by fusing PseAA composition and PsePSSM. Protein Eng Des Sel 2007, 20:561-567. 10.1093/protein/gzm057, 17993650.
3. Lei Z, Dai Y. Assessing protein similarity with Gene Ontology and its use in subnuclear localization prediction. BMC Bioinformatics 2006, 7:491. 10.1186/1471-2105-7-491, 17090318, 1660555.
4. Cedano J, Aloy P, P'erez-Pons J, Querol E. Relation between amino acid composition and cellular location of proteins. Journal of Molecular Biology 1997, 266:594-600. 10.1006/jmbi.1996.0804, 9067612.
5. Hoglund A, Donnes P, Blum T, Adolph H, Kohlbacher O. MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition. Bioinformatics 2006, 22(10):1158-1165. 10.1093/bioinformatics/btl002, 16428265.
6. Bhasin M, Raghava G. ELSpred: SVM-based method for subcellular localization of eukaryotic proteins using dipeptide composition and PSI-BLAST. Nucleic Acid Res 2004, (32 Web Server):W414-W419. 10.1093/nar/gkh350, 441488, 15215421.
7. Chou K. Prediction of protein subcellular locations by incorporating quasi-sequence-order effect. Biochemical and Biophysical Research Communications 2000, 278:477-483. 10.1006/bbrc.2000.3815, 11097861.
8. Lee K, Chuang H, Beyer A, Sung M, Huh W, Lee B, Ideker T. Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species. Nucleic Acids Research 2008, 36(20):e136. 10.1093/nar/gkn619, 2582614, 18836191.
9. Alexander Z, Cheng S. An. Automated combination of kernels for predicting protein subcellular localization. NIPS workshop on Machine Learning in Computational Biology 2007
10. Dijk A, Bosch D, Braak C, Krol A, Ham R. Predicting sub-Golgi localization of type II membrane proteins. Bioinformatics 2008, 24(16):1779-1786. 10.1093/bioinformatics/btn309, 18562268.
11. Shen J, Zhang J, Luo X, Zhu W, Yu K, Chen K, Li Y, Jiang H. Predicting protein-protein interactions based only on sequences information. PNAS 2007, 104(11):4337-4341. 10.1073/pnas.0607879104, 1838603, 17360525.
12. Schneider G, Fechner U. Review advances in the prediction of protein targeting signals. Proteomics 2004, 4:1571-1580. 10.1002/pmic.200300786, 15174127.
13. Edward M, Ioannis X, Alexander M, David E. Localizing proteins in the cell from their phylogenetic profiles. Proc Natl Acad Sci USA 2000, 97:12115-12120. 10.1073/pnas.220399497, 17303, 11035803.
14. Guo J, Lin Y. TSSub: eukaryotic protein subcellular localization by extracting features from profiles. Bioinformatics 2006, 22(14):1784-1785. 10.1093/bioinformatics/btl180, 16787975.
15. Mak M, Guo J, Kung S. PairProSVM: protein subcellular localization based on local pairwise profile alignment and SVM. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2008, 5(3):416-422.
16. Rangwala H, Karypis G. Profile-based direct kernels for remote homology detection and fold recognition. Bioinformatics 2005, 21(23):4239-4247. 10.1093/bioinformatics/bti687, 16188929.
17. Kuang R, Ie E, Wang K, Siddiqi M, Freund Y, Leslie C. Profile-based string kernels for remote homology detection and motif extraction. J Bioinform Comput Biol 2005, 3:527-550. 10.1142/S021972000500120X, 16108083.
18. Leslie C, Eskin E, Cohen A, Weston J, Noble W. Mismatch string kernels for discriminative protein classification. Bioinformatics 2004, 20(4):467-476. 10.1093/bioinformatics/btg431, 14990442.
19. Kuang R, Jianying G, Hong C, Yufeng W. Improved prediction of malaria degradomes by supervised learning with SVM and profile kernel. Genetica 2009, 136:189-209. 10.1007/s10709-008-9336-9, 19057851.
20. Richard M, Jörg S, Peer B, Chris P. Predicting protein cellular localization using a domain projection method. Genome Research 2002, 12:1168-1174. 10.1101/gr.96802, 186639, 12176924.
21. Jia P, Qian Z, Zeng Z, Cai Y, Li Y. Prediction of subcellular protein localization based on functional domain composition. Biochemical and Biophysical Research Communications 2007, 357:366-370. 10.1016/j.bbrc.2007.03.139, 17428441.
22. Mei S, Wang F. Structural domain based multiple instance learning for predicting bacteria Gram-positive protein subcelluar location. International Joint Conferences on Bioinformatics, Systems Biology and Intelligent Computing 2009
23. Chou K, Shen H. Cell-PLoc: A package of web-servers for predicting subcellular localization of proteins in various organisms. Nature Protocols 2008, 3:153-162. 10.1038/nprot.2007.494, 18274516.
24. Tung T, Lee D. A method to improve protein subcellular localization prediction by integrating various biological data sources. BMC Bioinformatics 2009, 10(Suppl 1):S43. 10.1186/1471-2105-10-S1-S43, 2648781, 19208145.
25. Leslie C, Eskin E, Noble W. The spectrum kernel: a string kernel for SVM protein classification. Proc Pac Biocomput Symp 2002, 7:566-575.
26. Taylor J, Cristianini N. Kernel Methods for Pattern Analysis. 2004, Cambridge University Press.
27. Vapnik V. Statistical Learning Theory. 1998, Springer.
28. Alejandro S, Ernesto P, Segovia L. Protein homology detection and fold inference through multiple alignment entropy profiles. Proteins 2008, 70:248-256. 10.1002/prot.21506, 17671981.
29. Lanckriet G, DeBie T, Cristianini N, Jordan M, Noble W. A statistical framework for genomic data fusion. Bioinformatics 2004, 20(16):2626-2635. 10.1093/bioinformatics/bth294, 15130933.
30. Boeckmann B, Bairoch A, Apweiler R, Blatter M, Estreicher A, Gasteiger E, Martin M, Michoud K, Donovan C, Phan I, et al. The SWISS-PROT protein knowledgebase and its Supplement TrEMBL. Nucleic Acids Research 2003, 31:365-370. 10.1093/nar/gkg095, 165542, 12520024.
31. Dellaire G, Farrall R, Bickmore W. The Nuclear Protein Database (NPD): subnuclear localisation and functional annotation of the nuclear proteome. Nucl Acids Res 2003, 31:328-330. 10.1093/nar/gkg018, 165465, 12520015.