Classification of protein sequences by means of irredundant patterns

BMC Bioinformatics

Volumn 11, Issue SUPPLL.1, 2010, Pages

  Comin, Matteo ^a   Verzotto, Davide ^a  

^a UNIVERSITY OF PADOVA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

BENCHMARK DATA; DISCRIMINATIVE METHODS; PROTEIN FUNCTION PREDICTION; PROTEIN SEQUENCES; STATE-OF-THE-ART METHODS; STRING ALGORITHMS; SUPPORT VECTOR;

ALGORITHMS; BIOINFORMATICS;

ALGORITHMS;

PROTEIN;

ALGORITHM; ARTICLE; CHEMISTRY; CLASSIFICATION; METHODOLOGY; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

ALGORITHMS; PROTEINS; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 75149191979     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-S1-S16     Document Type: Article

References (31)

1. Vinga S, Almeida J. Alignment-free sequence comparison - a review. Bioinformatics 2003, 19(4):513-523. 10.1093/bioinformatics/btg005, 12611807.
2. Gribskov M, McLachlan AD, Eisenberg D. Profile analysis: detection of distantly related proteins. Proc Natl Acad Sci U S A 1987, 84(13):4355-4358. 10.1073/pnas.84.13.4355, 305087, 3474607.
3. Krogh A, Brown M, Mian IS, Sjöolander K, Haussler D. Hidden Markov models in computational biology: applications to protein modeling. Journal of Molecular Biology 1994, 235:1501-1531. 10.1006/jmbi.1994.1104, 8107089.
4. Baldi P, Chauvin Y, Hunkapiller T, McClure M. Hidden Markov models of biological primary sequence information. Proc Natl Acad Sci U S A 1994, 91:1059-1063. 10.1073/pnas.91.3.1059, 521453, 8302831.
5. Karplus K, Barrett C, Hughey R. Hidden Markov models for detecting remote protein homologies. Bioinformatics 1998, 14:846-856. 10.1093/bioinformatics/14.10.846, 9927713.
6. Altschul SF, Madden TL, Schffer AA, Schaffer RA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 1997, 25:3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
7. Jaakkola T, Diekhans M, Haussler D. Using the Fisher kernel method to detect remote protein homologies. Proceedings of the 7th International Conference on Intelligent Systems for Molecular Biology (ISMB 1999) 1999, 149-158. AAAI, Thomas Lengauer, Richard Schneider, Peer Bork, Douglas L Brutlag, Janice I Glasgow, Hans-Werner Mewes and Ralf Zimmer.
8. Liao L, Noble WS. Combining pairwise sequence similarity and support vector machines for detecting remote protein evolutionary and structural relationships. Journal of Computational Biology 2003, 10:857-868. 10.1089/106652703322756113, 14980014.
9. Leslie CS, Eskin E, Noble WS. The spectrum kernel: a string kernel for SVM protein classification. Proceedings of the 7th Pacific Symposium on Biocomputing (PSB 2002) 2002, 564-575. Russ B Altman, A Keith Dunker, Lawrence Hunter and Teri E Klein.
10. Leslie CS, Eskin E, Cohen A, Weston J, Noble WS. Mismatch string kernels for discriminative protein classification. Bioinformatics 2004, 20(4):467-476. 10.1093/bioinformatics/btg431, 14990442.
11. Saigo H, Vert JP, Ueda N, Akutsu T. Protein homology detection using string alignment kernels. Bioinformatics 2004, 20(11):1682-1689. 10.1093/bioinformatics/bth141, 14988126.
12. Hou Y, Hsu W, Lee ML, Bystroff C. Efficient remote homology detection using local structure. Bioinformatics 2003, 19:2294-2301. 10.1093/bioinformatics/btg317, 14630658.
13. 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.
14. Kuang R, Ie E, Wang K, Wang K, Siddiqi M, Freund Y, Leslie C. Profile-based string kernels for remote homology detection and motif extraction. Journal of Bioinformatics and Computational Biology 2005, 3(3):527-550. 10.1142/S021972000500120X, 16108083.
15. Vapnik VN. Statistical Learning Theory 1998, Wiley-Interscience.
16. Ben-Hur A, Brutlag DL. Remote homology detection: a motif based approach. Bioinformatics 2003, 19(Suppl 1):i26-i33. 10.1093/bioinformatics/btg1002, 12855434.
17. Nevill-Manning CG, Wu TD, Brutlag DL. Highly specific protein sequence motifs for genome analysis. Proc Natl Acad Sci U S A 1998, 95:5865-5871. 10.1073/pnas.95.11.5865, 34488, 9600885.
18. Huang JY, Brutlag DL. The eMOTIF database. Nucleic Acids Research 2001, 29:202-204. 10.1093/nar/29.1.202, 29837, 11125091.
19. Haussler D. Convolution kernels on discrete structures. Technical Report 1999, (UCS-CRL-99-10). University of California at Santa Cruz, Santa Cruz, CA, USA.
20. Lingner T, Meinicke P. Word correlation matrices for protein sequence analysis and remote homology detection. BMC Bioinformatics 2008, 9:259. 10.1186/1471-2105-9-259, 2438326, 18522726.
21. Apostolico A, Tagliacollo C. Incremental discovery of the irredundant motif bases for all suffixes of a string in O(n2 log n) time. Theoretical Computer Science 2008, 408(2-3):106-115.
22. Apostolico A, Tagliacollo C. Optimal offline extraction of irredundant motif bases. Proceedings of the 13th Annual International Computing and Cobinatorics Conference (COCOON 2007) 2007, 4598:360-371. Springer, Lin G, Lecture Notes in Computer Science.
23. Apostolico A, Parida L. Incremental paradigms of motif discovery. Journal of Computational Biology 2004, 11:15-25. 10.1089/106652704773416867, 15072686.
24. Pisanti N, Crochemore M, Grossi R, Sagot MF. Bases of motifs for generating repeated patterns with wild cards. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2005, 2:40-50.
25. Comin M, Parida L. Detection of subtle variations as consensus motifs. Theoretical Computer Science 2008, 395(2-3):158-170.
26. Hulo N, Bairoch A, Bulliard V, Cerutti L, Cuche B, de Castro E, Lachaize C, Langendijk-Genevaux P, Sigrist C. The 20 years of PROSITE. Nucleic Acids Research 2008, (36 Database):D245-9. 2238851, 18003654.
27. Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A 1992, 89(22):10915-10919. 10.1073/pnas.89.22.10915, 50453, 1438297.
28. Eichhorn J. Applications of kernel machines to structured data. PhD thesis 2007, Technische Universität Berlin.
29. Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. Journal of Molecular Biology 1995, 247:536-540.
30. Noble WS, Pavlidis P. Gist support vector machine and kernel principal components analysis software toolkit. 2002, Columbia University.
31. Jaakkola T, Diekhans M, Haussler D. A discriminative framework for detecting remote protein homologies. Journal of Computational Biology 2000, 7:95-114. 10.1089/10665270050081405, 10890390.