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

Theory and Practice"


Monday, 6 January 1997


Morning Lectures

9:30 AM in silico Analyses: A History and An Introduction to Understanding DNA, RNA, and Proteins from a Bioinformatic Perspective; Bioinformatics versus Bio-Information Theory

"Genotype as Phenotype"

Why is computational molecular biology so difficult? How will an ever changing conception of what a "gene" is affect the sorts of molecular bioinformatic tools that we will need? What significance does in silico analysis of biological molecules have for the bench or field biologist or the industrial scientist? These questions will be addressed through five parallel pairs of considerations: Biologically, Linguistically, Computationally, Mathematically, Philosophically.

Bibliography

10:45 AM Break

11:15 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

"Being Digital"

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.


Bibliography

12:30PM - 2PM Lunch

Afternoon Laboratories
2 PMUse of Nucleic Acid Analysis Packages: Translation & Reverse-translation, Reading Frames, Coding and Non-coding regions, physico-chemical properties, Base/Codon statistics, etc. Web based data bases, searches and downloading.

SOFTWARE: SeqPup (MacOS, Windows, UNIX), NCBI (web)

3:30 PM Break

3:45 - 5 PM Continuation of the early afternoon session expanded to include other programs that do similiar things.

SOFTWARE: Sequence retrieval: ENTREZ (web), EBI/EMBL (web), SwissProt (web), Swiss-Shop (web [sequence notifier])


Software:

SeqPup

Description: A biological sequence editor and analysis program for the Macintosh, MS-Windows and UNIX platforms. It includes links to network services and external analysis programs.

Written by: Don Gilbert (Indiana University)

For more information: SeqPup readme

Webware:

Searching



NCBI (Genbank) Text Searching



NCBI Entrez Searching




EBI Text Searching





Swiss-Prot Text Search


Databases


Drosophila genome


Saccharomyces Genome Database (SGD)




C. elegans searching




Arabidopsis thaliana database searching






Maize Database





Rice Database






Email notification of sequences which are of interest to you!

Swiss-Shop Registration



Generally useful webtools:

BioSCI. Search/Read through helpful hints, address database, or post your own questions/answers to other peoples problems.

Need an email address for a colleague? Try: Who Where? or Four 11 White Pages or go directly to the College or University homepage .


Bibliography - Genotype as Phenotype

Jungck, John R. (1984). "Genotype as Phenotype: How Genetic Engineering has Changed Our Fundamental Concepts of Genetics. Amer. Biol. Teacher, 46 (7), October 1984, p. 357, 405.

Robbins, Robert J. (1994). "Representing Genomic Maps in a Relational Database," Pp. 85-96 in Suhai, Sándor, Ed., Computational Methods in Genome Research.

Hoffmeyer, Jesper. (1995). "The Swarming Cyberspace of the Body," Cybernetics & Human Knowing, 3:1-10. http

Steffen, David. (1996). "An Introduction to Biocomputing." Biocomputing Hypertext Coursebook. http://www.VSNS (BioComputing Home Page).

Wootton, John C. (1996). "Underdeveloped territories of bioinformatics." (Review of Steffan Schulze-Kremer's Molecular Bioinformatics: Algorithms and Applications). Nature Biotechnology 14:1303 (October).

Gibbs, Adrian. (1996). "Bioinformatics: A New Frontier in Biology." Australian National University, Research School of Biological Sciences, Canberra ACT 0200.

Wilson, Sue. (1996). "Biostatistics for the Molecular Age." Australian National University, Research School of Biological Sciences, Canberra ACT 0200.

Jungck, John R. (1977). "Complementarity and Coding." J. College Science Teaching, 7:27-28 (September).

"Database Artifacts." WEB Page.

States, D. J. and Botstein, D. 1991. "Molecular sequence accuracy and the analysis of protein coding regions." Proc. Natl. Acad. Sci. USA 88:5518-22.

Pevzner, Pavel A. "Genome rearrangements or what Dobzhansky and Sturtevant did not tell us." Department of Mathematics and Computer Science, University of Southern California.


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Bibliography - Being Digital: Genetic Codes as Codes

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


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Last modified: Wed Jan 1 11:26:05 1997