Twenty-five Years of Delila and Molecular Information Theory

Biological Theory

Volumn 1, Issue 3, 2006, Pages 250-260

  Schneider, Thomas D ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

Author keywords

Claude Shannon; DNA binding; information theory; replication sequence logo; sequence walker

Indexed keywords

EID: 77649263002     PISSN: 15555542     EISSN: 15555550     Source Type: Journal    
DOI: 10.1162/biot.2006.1.3.250     Document Type: Article

References (44)

1. Ban N, Nissen P, Hansen J, Moore PB, Steitz TA (2000) The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 289: 905–920. DOI: 10.1126/science.289.5481.905
2. Blattner FR, Plunkett III G, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y (1997) The complete genome sequence of Escherichia coli K-12. Science 277: 1453–1474. DOI: 10.1126/science.277.5331.1453
3. Crick FHC, Barnett L, Brenner S, Watts-Tobin RJ (1961) General nature of the genetic code for proteins. Nature 192: 1227–1232. DOI: 10.1038/1921227a0
4. Hengen PN, Bartram SL, Stewart LE, Schneider TD (1997) Information analysis of Fis binding sites. Nucleic Acids Research 25: 4994–5002. DOI: 10.1093/nar/25.24.4994
5. Herman ND, Schneider TD (1992) High information conservation implies that at least three proteins bind independently to F plasmid incD repeats. Journal of Bacteriology 174: 3558–3560.
6. Lewin B (1997) Genes VI. Oxford: Oxford University Press.
7. Lyakhov IG, Hengen PN, Rubens D, Schneider TD (2001) The P1 phage replication protein RepA contacts an otherwise inaccessible thymine N3 proton by DNA distortion or base flipping. Nucleic Acids Research 29: 4892–4900. DOI: 10.1093/nar/29.23.4892
8. Matten SR, Schneider TD, Ringquist S, Brusilow WSA (1998) Identification of an intragenic ribosome binding site that affects expression of the uncB gene of the Escherichia coli proton-translocating ATPase (unc) operon. Journal of Bacteriology 180: 3940–3945.
9. Nissen P, Hansen J, Ban N, Moore PB, Steitz TA (2000) The structural basis of ribosome activity in peptide bond synthesis. Science 289: 920–930. DOI: 10.1126/science.289.5481.920
10. Papp PP, Chattoraj DK, Schneider TD (1993) Information analysis of sequences that bind the replication initiator RepA. Journal of Molecular Biology 233: 219–230. DOI: 10.1006/jmbi.1993.1501
11. Pierce JR (1980) An Introduction to Information Theory: Symbols, Signals and Noise. 2nd ed. New York: Dover.
12. Pribnow D (1975) Nucleotide sequence of an RNA polymerase binding site at an early T7 promoter. Proceedings of the National Academy of Sciences USA 72: 784–788. DOI: 10.1073/pnas.72.3.784
13. Roberts RJ (1995) On base flipping. Cell 82: 9–12. DOI: 10.1016/0092-8674(95)90046-2
14. Roberts RJ, Cheng X (1998) Base flipping. Annual Review of Biochemistry 67: 181–198. DOI: 10.1146/annurev.biochem.67.1.181
15. Rogan PK, Faux BM, Schneider TD (1998) Information analysis of human splice site mutations. Human Mutation 12: 153–171. DOI: 10.1002/(SICI)1098-1004(1998)12:3<153::AID-HUMU3>3.0.CO;2-I
16. Rudd KE (2000) EcoGene: A genome sequence database for Escherichia coli K-12. Nucleic Acids Research 28: 60–64. DOI: 10.1093/nar/28.1.60
17. Schneider TD (1991a) Theory of molecular machines. I. Channel capacity of molecular machines. Journal of Theoretical Biology 148: 83–123. DOI: 10.1016/S0022-5193(05)80466-7
18. Schneider TD (1991b) Theory of molecular machines. II. Energy dissipation from molecular machines. Journal of Theoretical Biology 148: 125–137. DOI: 10.1016/S0022-5193(05)80467-9
19. Schneider TD (1995) Information Theory Primer.
20. Schneider TD (1997a) Information content of individual genetic sequences. Journal of Theoretical Biology 189: 427–441. DOI: 10.1006/jtbi.1997.0540
21. Schneider TD (1997b) Sequence walkers: A graphical method to display how binding proteins interact with DNA or RNA sequences. Nucleic Acids Research 25: 4408–1415. DOI: 10.1093/nar/25.21.4408
22. Schneider TD (1999) Measuring molecular information. Journal of Theoretical Biology 201: 87–92. DOI: 10.1006/jtbi.1999.1012
23. Schneider TD (2000) Evolution of biological information. Nucleic Acids Research 28: 2794–2799. DOI: 10.1093/nar/28.14.2794
24. Schneider TD (2001) Strong minor groove base conservation in sequence logos implies DNA distortion or base flipping during replication and transcription initiation. Nucleic Acids Research 29: 4881–4891. DOI: 10.1093/nar/29.23.4881
25. Schneider TD (2002a) Introduction to Delila Instructions. http://www.ccmp.ncifcrf.gov/∼toms/delilainstructions.html.
26. Schneider TD (2002b) The Atchange Program. http://www.ccrnp.ncifcrf.gov/∼toms/atchange.html.
27. Schneider TD, Mastronarde D (1996) Fast multiple alignment of ungapped DNA sequences using information theory and a relaxation method. Discrete Applied Mathematics 71: 259–268. DOI: 10.1016/S0166-218X(96)00068-6
28. Schneider TD, Rogan PK (1999) Computational analysis of nucleic acid information defines binding sites, United States Patent 5867402.
29. Schneider TD, Stephens RM (1990) Sequence logos: A new way to display consensus sequences. Nucleic Acids Research 18: 6097–6100. DOI: 10.1093/nar/18.20.6097
30. Schneider TD, Stormo GD (1989) Excess information at bacteriophage T7 genomic promoters detected by a random cloning technique. Nucleic Acids Research 17: 659–674. DOI: 10.1093/nar/17.2.659
31. Schneider TD, Stormo GD, Gold L, Ehrenfeucht A (1986) Information content of binding sites on nucleotide sequences. Journal of Molecular Biology 188: 415–431. DOI: 10.1016/0022-2836(86)90165-8
32. Schneider TD, Stormo GD, Haemer JS, Gold L (1982) A design for computer nucleic-acid sequence storage, retrieval and manipulation. Nucleic Acids Research 10: 3013–3024. DOI: 10.1093/nar/10.9.3013
33. Schneider TD, Stormo GD, Yarus MA, Gold L (1984) Delila system tools. Nucleic Acids Research 12: 129–140. DOI: 10.1093/nar/12.1Part1.129
34. Shannon CE (1948) A mathematical theory of communication. Bell System Technical Journal 27: 379–423, 623–656. DOI: 10.1002/j.1538-7305.1948.tb01338.x
35. Shine J, Dalgarno L (1974) The 3′-terminal sequence of Escherichia coli 16S ribosomal RNA: Complementarity to nonsense triplets and ribosome binding sites. Proceedings of the National Academy of Sciences USA 71: 1342–1346. DOI: 10.1073/pnas.71.4.1342
36. Shinedling S, Gayle M, Pribnow D, Gold L (1987) Mutations affecting translation of the bacteriophage T4 rIIB gene cloned in Escherichia coli. Molecular and General Genetics 207: 224–232. DOI: 10.1007/BF00331582
37. Shultzaberger RK, Bucheimer RE, Rudd KE, Schneider TD (2001) Anatomy of Escherichia coli ribosome binding sites. Journal of Molecular Biology 313: 215–228. DOI: 10.1006/jmbi.2001.5040
38. Singer BS, Gold L, Shinedling ST, Colkitt M, Hunter LR, Pribnow D, Nelson MA (1981) Analysis in vivo of translational mutants of the rIIB cistron of bacteriophage T4. Journal of Molecular Biology 149: 405–432. DOI: 10.1016/0022-2836(81)90479-4
39. Stephens RM, Schneider TD (1992) Features of spliceosome evolution and function inferred from an analysis of the information at human splice sites. Journal of Molecular Biology 228: 1124–1136. DOI: 10.1016/0022-2836(92)90320-J
40. Stormo GD, Schneider TD, Gold L, Ehrenfeucht A (1982a) Use of the “per-ceptron” algorithm to distinguish translational initiation sites in E. coli. Nucleic Acids Research 10: 2997–3011. DOI: 10.1093/nar/10.9.2997
41. Stormo GD, Schneider TD, Gold LM (1982b) Characterization of translational initiation sites in E. coli. Nucleic Acids Research 10: 2971–2996. DOI: 10.1093/nar/10.9.2971
42. Tribus M (1961) Thermostatics and Thermodynamics. Princeton, NJ: Van Nostrand.
43. Wimberly BT, Brondersen DE, Clemons Jr WM, Morgan-Warren RJ, Carter AP, Vonrheln C, Hartsch T, Ramakrishnan V (2000) Structure of the 30S ribosomal subunit. Nature 407: 327–339. DOI: 10.1038/35030006
44. Yusupova GZ, Yusupov MM, Cate JH, Noller HF (2001) The path of messenger RNA through the ribosome. Cell 106: 233–241. DOI: 10.1016/S0092-8674(01)00435-4