Sequence walkers: A graphical method to display how binding proteins interact with DNA or RNA sequences

Nucleic Acids Research

Volumn 25, Issue 21, 1997, Pages 4408-4415

  Schneider, Thomas D ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA BINDING PROTEIN; RNA BINDING PROTEIN;

ARTICLE; BINDING SITE; DNA SEQUENCE; GENETIC ENGINEERING; MACROMOLECULE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN NUCLEIC ACID INTERACTION; RNA SEQUENCE;

BASE SEQUENCE; DATABASES, FACTUAL; DNA; DNA-BINDING PROTEINS; MATHEMATICS; RNA; RNA-BINDING PROTEINS; SOFTWARE;

EID: 0030658850     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/25.21.4408     Document Type: Article

References (46)

1. Schneider, T.D. and Stephens. R.M. (1990) Nucleic Acids Res., 18, 6097-6100.
2. Papp, P.P., Chattoraj, D.K. and Schneider, T.D. (1993) J. Mol. Biol., 233, 219-230.
3. Papp, P.P. and Iyer, V.N. (1995) J. Mol. Biol., 246, 595-608.
4. Schneider, T.D. (1996) Methods Enzymol., 274, 445-455. ftp://ftp.ncifcrf.gov/pub/delila/oxyr.ps
5. Stephens, R.M. and Schneider, T.D. (1992) J. Mol. Biol., 228, 1124-1136.
6. Schneider, T.D. (1993) In Keller, P.R. and Keller, M.M. (Eds) Visual Cues -Practical Data Visualization. IEEE Press, Piscataway, NJ, USA. p. 64.
7. Pietrokovski, S., Henikoff, J.G. and Henikoff, S. (1996) Nucleic Acids Res., 24, 197-200.
8. Pietrokovski, S. (1996) Nucleic Acids Res., 24, 3836-3845.
9. Blom, N., Hansen, J., Blaas, D. and Brunak, S. (1996) Protein Sci., 5, 2203-2216.
10. Shaner, M.C., Blair, I.M. and Schneider, T.D. (1993) In Mudge, T.N., Milutinovic, V. and Hunter, L. (Eds) Proceedings of the Twenty-Sixth Annual Hawaii International Conference on System Sciences. Volume I: Architecture and Biotechnology Computing. IEEE Computer Society Press, Los Alamitos, CA, USA. http://www-lmmb.ncifcrf.gov/~toms/ paper/hawaii/ pp. 813-821.
11. Staden, R. (1984) Nucleic Acids Res., 12, 505-519.
12. Stormo, G.D., Schneider, T.D., Gold, L. and Ehrenfeucht, A. (1982) Nucleic Acids Res., 10, 2997-3011.
13. Stormo, G.D., Schneider, T.D. and Gold, L. (1986) Nucleic Acids Res., 14, 6661-6679.
14. Stormo, G.D. (1990) Methods Enzymol., 183, 211-221.
15. Pierce, J.R. (1980) An Introduction to Information Theory: Symbols, Signals and Noise. Second Edition. Dover Publications, Inc., New York, NY, USA.
16. Sloane, N.J.A. and Wyner, A.D. (1993) Claude Elwood Shannon: Collected Papers. IEEE Press, Piscataway, NJ, USA.
17. Schneider, T.D. (1995) Information Theory Primer. http://www-lmmb.ncifcrf.gov/~toms/paper/primer/
18. Schneider, T.D. (1997) J. Theor. Biol., In press.
19. Schneider, T.D., Stormo, G.D., Haemer, J.S. and Gold, L. (1982) Nucleic Acids Res., 10, 3013-3024.
20. Schneider, T.D., Stormo, G.D., Yarus, M.A. and Gold, L. (1984) Nucleic Acids Res., 12, 129-140.
21. Schneider, T.D. and Mastronarde, D. (1996) Discrete Appl. Math., 71, 259-268. ftp://ftp.ncifcrf.gov/pub/delila/malign.ps
22. Schneider, T.D., Stormo, G.D., Gold, L. and Ehrenfeucht, A. (1986) J. Mol. Biol., 188, 415-431.
23. Hengen, P.N., Bartram, S.L., Stewart, L.E. and Schneider, T.D. (1997) Nucleic Acids Res., In press.
24. Jensen, K. and Wirth, N. (1975) Pascal User Manual and Report. Springer-Verlag, New York, NY, USA.
25. Adobe Systems Incorporated (1985) PostScript Language Reference Manual. Addison-Wesley Publishing Company, Reading, MA, USA.
26. Adobe Systems Incorporated (1985) PostScript Language Tutorial and Cookbook. Addison-Wesley Publishing Company, Reading, MA, USA.
27. Shannon, C.E. (1948) Bell System Tech. J., 27, 379-423 and 623-656.
28. Schneider, T.D. (1991) J. Theor. Biol., 148, 83-123. http://www-lmmb.ncifcrf.gov/~toms/paper/ccmm/
29. Schneider, T.D. (1994) Nanotechnology, 5, 1-18. http://www-Immb.ncifcrf.gov/~toms/paper/nano2/
30. Schneider, T.D. (1991) J. Theor. Biol., 148, 125-137. http://www-lmmb.ncifcrf.gov/~toms/paper/edmm/
31. Slany, R.K. and Kersten, H. (1992) Nucleic Acids Res., 20, 4193-4198.
32. Finkel, S.E. and Johnson, R.C. (1992) Mol. Microbiol., 6, 3257-3265.
33. Finkel, S.E. and Johnson, R.C. (1992) Mol. Microbiol., 6, 1023.
34. Goodrich, J.A., Schwartz, M.L. and McClure, W.R. (1990) Nucleic Acids Res., 18, 4993-5000.
35. Sanger, F., Coulson, A.R., Hong, G.F., Hill, D.F. and Petersen, G.B. (1982) J. Mol. Biol., 162, 729-773.
36. Landy, A. and Ross, W. (1977) Science, 197, 1147-1160.
37. Thompson, J.F., deVargas, L.M., Koch, C., Kahmann, R. and Landy, A. (1987) Cell, 50, 901-908.
38. Ball, C.A. and Johnson, R.C. (1991) J. Bacteriol., 173, 4027-4031.
39. Ball, C.A. and Johnson, R.C. (1991) J. Bacteriol., 173, 4032-4038.
40. Numrych, T., Gumport, R.I. and Gardner, J.F. (1992) EMBO J., 11, 3797-3806.
41. Fishel, R., Lescoe, M.K., Rao, M.R.S., Copeland, N.G., Jenkins, N.A., Garber, J., Kane, M. and Kolodner, R. (1993) Cell, 75, 1027-1038.
42. Rogan, P.K. and Schneider, T.D. (1995) Human Mut., 6, 74-76.
43. Leach, F.S., Nicolaides, N.C., Papadopoulos, N., Liu, B., Jen, J., Parsons, R., Peltomäki, P., Sistonen, P., Aaltonen, L.A., Nyström-Lahti, M. et al. (1993) Cell, 75, 1215-1225.
44. Hübner, P. and Arber, W. (1989) EMBO J., 8, 577-585.
45. Landy, A. (1989) Annu. Rev. Biochem., 58, 913-949.
46. Thompson, J.F., Fong, H., Mark, L., Franz, B. and Landy, A. (1988) In Olson, W.K., Sarma, M.H., Sarma, R.H. and Sundaralingam, M. (Eds) Structure and Expression. Volume 3: DNA Bending and Curvature. Adenine Press, New York, NY, USA. pp. 119-128.