"in silico DNA, RNA, Protein Sequence,
and Structure Analysis:
Theory and Practice"

9:30 AM Genetic Codes as Codes: Huffman Codes (Fractals and Power Laws), Gray Codes, Hamming Codes, Baudot Codes, Comma-free Codes, Commaless Codes, and Overlapping Codes; Grantham Hypothesis

Mathematical properties of genetic codes will be demostrated with respect to their efficiencies, rates of transmission, correctability and detactability of errors, symmetries, and origins by employing codig theory (Baudot codes, Gray codes, Hamming codes, Huffman codes, common free codes, etc.), abstract algebra, graph theory, combinatorics, information theory, and phylogenetic systematics of sequences. Genetic codes becore much more understandable and elegant to biologists when they are not considered as mere ciphers, but are instead understood from three perspectives: codes per se, physical chemical interactions, and evolutionary selective pressures. In addition, I will illustrate some of the alternative distance metrics based upon different mathematical represenntations of genetic codes which have utility in genomic data base searching (comparative sequence analyses) and considerations of different evolutioary mechanisms.

Between genetic mapping in the traditional sense of assigning chromosomal locations to loci for particular polypeptides and the the level of complete nucleotide sequences, there is a need for a middle level of physical mapping. Can we completely order restriction fragments to cover a whole chromosome? Can we do this without knowing the exact lengths of each of the fragments or what loci they contain? Interval graphs and an associated piece of software that we have developed (BENZER) will be introduced so that a qualitative approach (topological) can be understood to this important problem. Even if you have very good quantitative information, in the last analysis, a determination of whether fragments overlap one another is necessary to understand the ordering of fragments. Several other software packages have also adopted the interval graph approach and will be introduced. Other molecular biological applications of interval graphs include sequencing, complementation mappping, and deletion mapping.

Jungck, John R. 1978. "The Genetic Code as a Periodic Table." J. of Mol. Evol. 1:211-224.

Bertman, Martha O. and Junngck, John R. 1979. "Group Graph of the Genetic Code." J. of Heredity 70:379-384.

Jungck, John R. 1984. "The Adaptationist Programme inn Molecular Evolution: The Origins of Genetic Codes," Pp. 345-364 in Matsuno, Koichiro et al., Eds., Molecular Evolution and Protobiology, Plenum Publishing Corporation.

Schneider, Thomas D. (1995). "Information Theory Primer." National Cancer Institute, Building 469, Room 144, P. O. Box B, Frederick, MD 21702-1201. http://www-lmmb.ncifcrf.gov/~tims/papers.html. Anonymous ftp site: ftp.ncifcrf.gov in the directory pub/delila

Jungck, John R. and Streif, Vince. 1986. "Deletion Mapping of Genetic 'Fine Structure': Supplementing Ad Hoc Problem Solving Approaches with Algorithms and Heuristics." Midwest Bioscene 12(2):-17.

Streif, Vince and Jungck, John R. 1982. "Benzer Problem Generator." Version 4.12 Alpha (November).

Mundt, M., Faber, V., Goldberg, M., Rivenburg, R., Soderlund, C. and Torney, D. "Interval Graphs and Interactive Graphics for Resolving Ambiguities in Overlap Data." Computing and Communications Group, Los Alamos National laboratory, Los Alamos, NM 87545.

Engle, M. L., Soderlund, C. A., Stolorz, P. E., and Burks, C. "Exploring DNA Fragment Assembly Problems: Benchmarks and Stochastic Solutions." Theoretical Biology and Biophysics Group (T-10, MS K710) Los Alamos National Laboratory, Los Alamos, NM 87545.

About SIGMA: "System for Integrated Genome Map Assembly."

Setubal, JoŅo C. and Meidanis, JoŅo. 1997. Introduction to Computational Molecular Biology. Table of Contents. PWS Publishing Company. 320 pp.

Murray, Darrel L. "How to Construct a Restriction Map."