Automatic prediction of protein domains from sequence information using a hybrid learning system

Bioinformatics

Volumn 20, Issue 9, 2004, Pages 1335-1360

  Nagarajan, Niranjan ^a   Yona, Golan ^a  

^a Department of Computer Science and School of Operations Research and Information Engineering   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; ARTIFICIAL NEURAL NETWORK; AUTOMATION; CALCULATION; CONTROLLED STUDY; CORRELATION ANALYSIS; INTERMETHOD COMPARISON; LEARNING; PREDICTION; PRIORITY JOURNAL; PROBABILITY; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN STRUCTURE; QUANTITATIVE ANALYSIS; SCORING SYSTEM; SENSITIVITY ANALYSIS; SEQUENCE ALIGNMENT; SEQUENCE DATABASE;

EID: 3142680264     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bth086     Document Type: Article

References (49)

1. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
2. Apweiler,R., Attwood,T.K., Bairoch,A., Bateman,A., Birney,E., Biswas,M., Bucher,P., Cerutti,L., Corpet,F., Croning,M.D. et al. (2001) The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res., 29, 37-40.
3. Bairoch,A. and Apweiler,R. (1999) The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999. Nucleic Acids Res., 27 49-54.
4. Bateman,A., Birney,E., Durbin,R., Eddy,S.R., Finn R.D. and Sonnhammer E.L. (1999) PFam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins. Nucleic Acids Res., 27, 260-262.
5. Black,S.D. and Mould,D.R. (1991) Development of hydrophobicity parameters to analyze proteins which bear post or cotranslational modifications. Anal. Biochem., 193, 72-82.
6. Csiszár,I. (1997) Information Theoretic Methods in Probability and Statistics.
7. Dembo,A. and Karlin,S. (1991) Strong limit theorems of empirical functionals for large exceedances of partial sums of i.i.d variables. Ann. Prob., 19, 1737-1755.
8. Ferran,E.A., Pflugfelder,B. and Ferrara,P. (1994) Self-organized neural maps of human protein sequences. Protein Sci., 3, 507-521.
9. George,R.A. and Heringa,J. (2002a) Protein domain identification and improved sequence similarity searching using PSI-BLAST. Proteins, 48, 672-681.
10. George,R.A. and Heringa,J. (2002b) SnapDRAGON: a method to delineate protein structural domains from sequence data. J. Mol. Biol., 316, 839-851.
11. George,D.G., Barker,W.C., Mewes,H.W., Pfeiffer,F. and Tsugita,A. (1996) The PIR-International protein sequence database. Nucleic Acids Res., 24, 17-20.
12. Gilbert,W. and Glynias,M. (1993) On the ancient nature of introns. Gene, 135, 137-144.
13. Gilbert,W., de Souza,S.J. and Long,M. (1997) Origin of genes. Proc. Natl Acad. Sci., USA, 94, 7698-7703.
14. Gouzy,J., Corpet,F. and Kahn,D. (1999) Whole genome protein domain analysis using a new method for domain clustering. Comput. Chem., 23, 333-340.
15. Gracy,J. and Argos,P. (1998) Automated protein sequence database classification. I. Integration of copositional similarity search, local similarity search and multiple sequence alignment. II. Delineation of domain boundries from sequence similarity. Bioinformatics, 14, 164-187.
16. Guan,X. and Du,L. (1998) Domain identification by clustering sequence alignments. Bioinformatics, 14, 783-788.
17. Ireland,C.T. and Kullback,S. (1968) Contingency tables with given marginals. Biometrika, 55, 179-189.
18. Haft,D.H., Loftus,B.J., Richardson,D.L., Yang,F., Eisen,J.A., Paulsen,I.T. and White,O. (2001) TIGRFAMs: a protein family resource for the functional identification of proteins. Nucleic Acids Res., 29, 41-43.
19. Henikoff,S. and Henikoff,J.G. (1992) Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci., USA, 89, 10915-10919.
20. Henikoff,S. and Henikoff,J.G. (1994) Position-based sequence weights. J. Mol. Biol., 243, 574-578.
21. Henikoff,J.G. and Henikoff,S. (1996) Using substitution probabilities to improve position-specific scoring matrices. Comput. Appl. Biosci., 12:2, 135-143.
22. Holm,L. and Sander,C. (1994) Parser for protein folding units. Proteins, 19, 256-268.
23. Hubbard,T.J., Ailey,B., Brenner,S.E., Murzin,A.G. and Chothia,C. (1999) SCOP: a structural classification of proteins database. Nucleic Acids Res., 27, 254-256.
24. Karlin,S. and Altschul,S.F. (1990) Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl Acad. Sci., USA, 87, 2264-2268.
25. Kullback,S. (1959) Information Theory and Statistics. John Wiley and Sons, New York.
26. Kuroda,Y., Tani,K., Matsuo,Y. and Yokoyama,S. (2000) Automated search of natively folded protein fragments for high-throughput structure determination in structural genomics. Protein Sci., 9, 2313-2321.
27. Lesk,A.M. and Rose,G.D. (1981) Folding units in globular proteins. Proc. Natl Acad. Sci., USA, 78, 4304-4308.
28. Lin,J. (1991) Divergence measures based on the Shannon entropy. IEEE Trans. Info. Theory, 37, 145-151.
29. McGuffin,L.J., Bryson,K. and Jones,D.T. (2000) The PSIPRED protein structure prediction server. Bioinformatics, 16, 404-405.
30. Miyazaki,S., Kuroda,Y. and Yokoyama,S. (2002) Characterization and prediction of linker sequences of multi-domain proteins by a neural network. J. Struct. Func. Genom., 15, 37-51.
31. Murvai,J., Vlahovicek,K., Szepesvari,C. and Pongor,S. (2001) Prediction of protein functional domains from sequences using artificial neural networks. Genome Res., 11, 1410-1417.
32. Murzin,A.G., Brenner,S.E., Hubbard,T. and Chothia,C. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
33. Orengo,C.A., Michie,A.D., Jones,S., Jones,D.T., Swindells,M.B. and Thornton,J.M. (1997) CATH - a hierarchic classification of protein domain structures. Structure, 5, 1093-1108.
34. Park,J. and Teichmann,S.A. (1998) DIVCLUS: an automatic method in the GEANFAMMER package that finds homologous domains in single- and multi-domain proteins. Bioinformatics, 14, 144-150.
35. Pazos,F., Helmer-Citterich,M., Ausiello,G. and Valencia,A. (1997) Correlated mutations contain information about protein-protein interaction. J. Mol. Biol., 271, 511-523.
36. Pearl,J. (1997) Probabilistic Reasoning in Intelligent Systems: Networks of Plausible Inference. Morgan Kaufmann Publishers Inc., San Mateo, California.
37. Pearson,W.R. and Lipman,D.J. (1988) Improved tools for biological sequence comparison. Proc. Natl Acad. Sci., USA, 85, 2444-2448.
38. Ponting,C.P., Schultz,J., Milpetz,F. and Bork,P. (1999) SMART: identification and annotation of domains from signalling and extracellular protein sequences. Nucleic Acids Res., 27, 229-232.
39. Rigden,D.J. (2002) Use of covariance analysis for the prediction of structural domain boundaries from multiple protein sequence alignments. Protein Eng., 15, 65-77.
40. Rose,G.D. (1979) Hierarchic organization of domains in globular proteins. J. Mol. Biol., 134, 447-470.
41. Saxonov,S., Daizadeh,I., Fedorov,A. and Gilbert,W. (2000) EID: the Exon-Intron Database - an exhaustive database of protein-coding intron-containing genes. Nucleic Acids Res., 28, 185-190.
42. Sonnhammer,E.L.L. and Kahn,D. (1994) Modular arrangement of proteins as inferred from analysis of homology. Protein Sci., 3, 482-492.
43. Sonnhammer,E.L., Eddy,S.R. and Durbin,R. (1997) PFam: a comprehensive database of protein domain families based on seed alignments. Proteins, 28, 405-420.
44. Sowdhamini,R. and Blundell,T.L. (1995) An automatic method involving cluster analysis of secondary structures for the identification of domains in proteins. Protein Sci., 4, 506-520.
45. Taylor,W.R. (1999) Protein structural domain identification. Protein Eng., 12, 203-216.
46. Westbrook,J., Feng,Z., Jain,S. et al. (2002) The Protein Data Bank: unifying the archive. Nucleic Acids Res., 30, 245-248.
47. Wheelan,S.J., Marchier-Bauer,A. and Bryant,S.H. (2000) Domain size distributions can predict domain boundaries. Bioinformatics, 16, 613-618.
48. Yona,G. and Levitt,M. (2000) Towards a complete map of the protein space based on a unified sequence and structure analysis of all known proteins. Proceedings of ISMB 2000. AAAI Press, Menlo Park, pp. 395-406.
49. Yona,G., Linial,N. and Linial,M. (1999) ProtoMap: automatic classification of protein sequences, a hierarchy of protein families, and local maps of the protein space. Proteins, 37, 360-378.