Complementary classification approaches for protein sequences

Protein Engineering

Volumn 9, Issue 5, 1996, Pages 381-386

  Wang, Jason T L ^a   Marr, Thomas G ^b   Shasha, Dennis ^c   Shapiro, Bruce A ^d   Chirn, Gung Wei ^a   Lee, T Y ^e  

^a NEW JERSEY INSTITUTE OF TECHNOLOGY   (United States)

^b Watson School of Biological Sciences   (United States)

^c NEW YORK UNIVERSITY   (United States)

^d NATIONAL INSTITUTES OF HEALTH   (United States)

^e UNIVERSITY OF MARYLAND   (United States)

Author keywords

Block searching; Protein classification; Protein database; Statistical approaches; SWISS PROT

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; CLASSIFICATION; DATA BASE; PRIORITY JOURNAL; PROTEIN FAMILY; SEQUENCE HOMOLOGY;

EID: 0029951408     PISSN: 02692139     EISSN: None     Source Type: Journal    
DOI: 10.1093/protein/9.5.381     Document Type: Article

References (38)

1. Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) J. Mol. Biol., 215, 403-410.
2. Altschul,S.F. and Lipman,D.J. (1990) Proc. Natl Acad. Sci. USA, 87, 5509-5513.
3. Bairoch,A. (1989) PROSITE: A Dictionary Of Protein Sites and Patterns. EMBL, release 4.
4. Bairoch,A. (1992) Nucleic Acids Res., 20, 2013-2018.
5. Bairoch,A. and Boeckmann,B. (1992) Nucleic Acids Res., 20, 2019-2022.
6. Berg,O.G. and von Hippel,P.H. (1987) J. Mol. Biol., 193, 723-750.
7. Brown,M., Hughey,R., Krogh,A., Mian,I.S., Sjolander,K. and Haussler,D. (1993) In Hunter,L., Searls,D. and Shavlik,J. (eds), Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology. AAAI, Menlo Park, CA, pp. 47-55.
8. Califano,A. and Rigoutsos,I. (1993) In Hunter,L., Searls,D. and Shavlik,J. (eds), Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology. AAAI, Menlo Park, CA.
9. Dayhoff,M.O., Schwartz,R.M. and Orcutt,B.C. (1978) In Dayhoff,M.O. (ed.), Atlas of Protein Sequence and Structure. National Biomedical Research Foundation, Washington, DC, Vol. 5. Suppl. 3, pp. 345-352.
10. Dodd,I. and Egan,J.B. (1990) Nucleic Acids Res., 18, 5019-5026.
11. Duda,R.O. and Hart,P.E. (1973) Pattern Classification and Scene Analysis. Wiley, New York.
12. Gish,W. and States,D.J. (1993) Nature Genet., 3, 266-272.
13. Gribskov,M., McLachlan,A.D. and Eisenberg,D. (1987) Proc. Natl Acad. Sci. USA, 84, 4355-4358.
14. Henikoff,S. and Henikoff,J.G. (1991) Nucleic Acids Res., 19, 6565-6572.
15. Henikoff,S. and Henikoff,J.G. (1992) Proc. Natl Acad. Sci. USA, 89, 10915-10919.
16. Henikoff,S. and Henikoff,J.G. (1993) Proteins: Struct. Funct. Genet., 17, 49-61.
17. Henikoff,S. and Henikoff,J.G. (1994) Genomics, 19, 97-107.
18. Henikoff,S., Wallace,J.C. and Brown,J.P. (1990) Methods Enzymol., 183, 111-132.
19. Henikoff,S., Henikoff,J.G., Agus,S. and Wallace,J.C. (1993) In Venter,J.C. (ed.), Automated DNA Sequencing and Analysis Techniques. Academic Press, London, UK.
20. Henikoff,S., Henikoff,J.G., Alford,W.J. and Pietrokovski,S. (1995) Gene-Combis, 163, GC17-GC26.
21. Hodgman,T.C. (1989) CABIOS, 5, 1-13.
22. Jones,D.T., Taylor,W.R. and Thornton,J.M. (1992) CABIOS, 8, 275-282.
23. Karlin,S. and Altschul,S.F. (1990) Proc. Natl Acad. Sci. USA, 87, 2264-2268.
24. Lawrence,C.E., Altschul,S.F., Boguski,M.S., Liu,J.S., Neuwald,A.F. and Wootton,J.C. (1993) Science, 262, 208-214.
25. Ogiwara,A., Uchiyama,I., Seto,Y. and Kanehisa,M. (1992) Protein Engng, 5, 479-488.
26. Schneider,T.S., Stormo,G.D., Gold,L. and Ehrenfeucht,A. (1986) J. Mol. Biol., 188, 415-431.
27. Schwartz,R.M. and Dayhoff,M.O. (1978) In Dayhoff,M.O. (ed.), Atlas of Protein Sequence and Structure. National Biomedical Research Foundation, Washington, DC, Vol. 5, Suppl. 3, pp. 353-358.
28. Seto,Y., Ikeuchi,Y. and Kanehisa,M. (1990) Proteins, 8, 341-351.
29. Smith,R.F. and Smith,J.F. (1990) Proc. Natl Acad. Sci. USA, 87, 118-122.
30. Staden,R. (1990) Methods Enzymol., 183, 193-211.
31. Stormo,G.D. and Hartzell,G.W.III (1989) Proc. Natl Acad. Sci. USA, 86, 1183-1187.
32. Tatusov,R.L. and Koonin,E.V. (1994) CABIOS, 10, 457-459.
33. Tatusov,R.L., Altschul,S.F. and Koonin,E.V. (1994) Proc. Natl Acad. Sci. USA, 91, 12091-12095.
34. Taylor,W.R. (1986) J. Mol. Biol., 188, 233-258.
35. Taylor,W.R. (1988) Protein Engng, 2, 77-86.
36. Wallace,J.C. and Henikoff,S. (1992) CABIOS, 8, 249-254.
37. Wang,J.T.L., Marr,T.G., Shasha,D., Shapiro,B. and Chim,G.-W. (1994) Nucleic Acids Res., 22, 2769-2775.
38. Zipf,G.K. (1949) Human Behavior and the Principle of Least Effort. Addison Wesley, Reading, MA.