Application of latent semantic analysis to protein remote homology detection

Bioinformatics

Volumn 22, Issue 3, 2006, Pages 285-290

  Dong, Qi Wen ^a   Wang, Xiao Long ^a   Lin, Lei ^a  

^a HARBIN INSTITUTE OF TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CLASSIFICATION; COMPARATIVE STUDY; COMPUTER ANALYSIS; COMPUTER LANGUAGE; COMPUTER PROGRAM; GENE VECTOR; INFORMATION PROCESSING; NOISE REDUCTION; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN FAMILY; PROTEIN MOTIF; SEMANTICS; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STRUCTURAL PROTEOMICS;

EID: 32144458563     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti801     Document Type: Article

References (35)

1. Altschul,S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
2. Altschul,S.F. et al. (1997) Gapped Blast and Psi-blast: A new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
3. Anand,B. et al. (2005) Use of multiple profiles corresponding to a sequence alignment enables effective detection of remote homologues. Bioinformatics, 21, 2821-2826.
4. Andreeva,A. et al. (2004) SCOP database in 2004: Refinements integrate structure and sequence family data. Nucleic Acids Res., 32, D226-D229.
5. Bailey,T.L. and Elkan,C. (1994) Filling a mixture model by expectation maximization to discover motifs in biopolymers. In Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, Menlo Park, California. pp. 28-36.
6. Bailey,T.L. and Grundy,W.N. (1999) Classifying proteins by family using the product of correlated p-values. In Proceedings of the Third International Conference on Computational Molecular Biology (RECOMB99), Lyon, France, pp. 10-14.
7. Bellegarda,J. (2000) Exploiting latent semantic information in statistical language modeling. Proc. IEEE, 88, 1279-1296.
8. Ben-Hur,A. and Brutlag, D. (2003) Remote homology detection: A motif based approach. Bioinformatics, 19(Suppl 1), i26-i33.
9. Chandonia,J.M. et al. (2004) The ASTRAL Compendium in 2004. Nucleic Acids Res., 32, 189-192.
10. Cheng,B.Y. et al. (2005) Protein classification based on text document classification techniques. Proteins, 58, 955-970.
11. Coin,L. et al. (2003) Enhanced protein domain discovery by using language modeling techniques from speech recognition. Proc. Natl Acad. Sci. USA, 100, 4516-4520.
12. Dong,Q.W. et al. (2005) A pattern-based SVM for protein remote homology detection. In The Fourth International Conference on Machine Learning and Cybernetics, GuangZhou, China, pp. 3363-3368.
13. Ganapathiraju,M. et al. (2005) Computational Biology and Language. Ambient Intelligence for Scientific Discovery, LNAI, 3345, 25-47.
14. Ganapathiraju,M. et al. (2004) Characterisation of protein secondary structure, Application of latent semantic analysis using different vocabularies. IEEE Signal Processing Magazine, 21, 78-87.
15. Ganapathiraju,M. et al. (2002) Comparative N-gram analysis of whole-genome protein sequences. In Proceedings of the Human Language. Technologies Conference, San Diego.
16. Gribskov,M. and Robinson,N.L. (1996) use of receiver operating characteristic(ROC) analysis to evaluate sequence matching. Comput. Chem., 20, 25-33.
17. Han,S. et al. (2005) Fold recognition by combining profile-profile alignment and support vector machine. Bioinformatics, 21, 2667-2673.
18. Hou,Y. et al. (2004) Remote homolog detection using local sequence-structure correlations. Proteins, 57, 518-530.
19. Hou,Y. et al. (2003) Efficient remote homology detection using local structure. Bioinformatics, 19, 2294-2301.
20. Jaakkola,T. et al. (2000) A discriminative framework for detecting remote protein homologies. J. Comput. Biol., 7, 95-114.
21. Karplus,K. et al. (1998) Hidden Markov models for detecting remote protein homologies. Bioinformatics, 14, 846-856.
22. Krogh,A. et al. (1994) Hidden Markov models in computational biology: applications to protein modeling. J. Mol. Biol., 235, 1501-1531.
23. Landauer,T.K. et al. (1998) Introduction to latent semantic analysis. Discourse Process, 25, 259-284.
24. Leslie,C. et al. (2004) Mismatch string kernels for discriminative protein classification. Bioinformatics, 20, 467-476.
25. Leslie,C., Eskin,E. and Noble,W.S. (2002) The spectrum kernel: A string kernel for SVM protein classification. In Proceedings of the Pacific Symposium on Biocomputing, Hawaii, USA, pp. 564-575.
26. Li,L. and Noble,W.S. (2003) Combining pairwise sequence similarity and support vector machines for detecting remote protein evolutionary and structural relationships. J. Comput. Boil., 10. 857-866.
27. Pearson,W.R. (1990) Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol., 183, 63-98.
28. Pisanti,N., Crochemore,M., Grossi,R. and Sagot,M.F. (2002) A basis for repeated motifs in pattern discovery and text mining. IGM 2002-10, Juillet.
29. Qian,B. and Goldstein,R.A. (2004) Performance of an iterated T-HMM for homology detection. Bioinformatics, 20, 2175-2180.
30. Rigoutsos,I. and Floratos,A. (1998) Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm. Bioinformatics, 14, 55-67.
31. Saigo,H. et al. (2004) Protein homology detection using string alignment kernels. Bioinformatics, 20, 1682-1689.
32. Saigo,H. et al. (2002) Comparison of SVM-based methods for remote homology detection. Genome Inform, 13, 396-397.
33. Smith,T.F. and Waterman,M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
34. Thompson,J.D. et al. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
35. Vapnik,V.N. (1998) Statistical Learning Theory. Wiley, New York.