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"Theoretical and computational methods in genome research"

PREFACE

The application of computational methods to solve scientific and practical problems in genome research created a new interdisciplinary area that transcends boundaries traditionally separating genetics, biology, mathematics, physics, and computer science. Computers have, of course, been intensively used in the field of life sciences for many years, even before genome research started, to store and analyze DNA or protein sequences; to explore and model the three-dimensional structure, the dynamics, and the function of biopolymers; to compute genetic linkage or evolutionary processes; and more. The rapid development of new molecular and genetic technologies, combined with ambitious goals to explore the structure and function of genomes of higher organisms, has generated, however, not only a huge and exponentially increasing body of data but also a new class of scientific questions. The nature and complexity of these questions will also require, beyond establishing a new kind of alliance between experimental and theoretical disciplines, the development of new generations both in computer software and hardware technologies.

New theoretical procedures, combined with powerful computational facilities, will substantially extend the horizon of problems that genome research can attack with success. Many of us still feel that computational models rationalizing experimental findings in genome research fulfill their promises more slowly than desired. There is also an uncertainty concerning the real position of a "theoretical genome research" in the network of established disciplines integrating their efforts in this field. There seems to be an obvious parallel between the present situation of genome research and that of atomic physics at the end of the first quarter of our century. Advanced experimental techniques made it possible at that time to fill huge data catalogues with the frequencies of spectral lines, yet all attempts at an empirical systematization or classically founded explanation remained unsuccessful until a completely new conceptual framework, quantum mechanics, emerged that made sense of all the data.

The present situation of the life sciences is certainly more intricate due to the more amorphous nature of the field. One has to ask whether it is a fair demand at all that genome research should reach the internal coherence of a unifying theoretical framework like theoretical physics or (to a smaller extent) chemistry. The fear seems to be, however, not unjustified that genomic data accumulation will get so far ahead of its assimilation into an appropriate theoretical framework that the data themselves might eventually prove an encumbrance in developing such new concepts. The aim of most of the computational methods presented in this volume is to improve upon this situation by trying to provide a bridge between experimental databases (information) on the one hand and theoretical concepts (biological and genetic knowledge) on the other.

The content of this volume was presented as plenary lectures at the International Symposium on Theoretical and Computational Genome Research held March 24-27, 1996, at the Deutsches Krebsforschungszentrum (DKFZ) in Heidelberg. It is a great pleasure to thank here Professor Harald zur Hausen and the coworkers of DKFZ for their help and hospitality extended to the lecturers and participants during the meeting and the Commission of the European Communities for the funding of the symposium. The organizers profited much from the help of the scientific committee of the symposium: Martin Bishop, Philippe Dessen, Reinhold Haux, Ralf Hofestädt, Willi Jäger, Jens G. Reich, Otto Ritter, Petre Tautu, and Martin Vingron. Furthermore, the editor is deeply indebted to Michaela Knapp-Mohammady and Anke Retzmann for their help in organizing the meeting and preparing this volume.

Sándor Suhai
Heidelberg, July 1996


CONTENTS

1. Evaluating the Statistical Significance of Multiple Distinct Local Alignments
Stephen F. Altschul
2. Hidden Markov Models for Human Genes: Periodic Pattems in Exon Sequences
Pierre Baldi, Søren Brunak, Yves Chauvin, and Anders Krogh
3. Identification of Muscle-Specific Transcriptional Regulatory Regions
James W. Fickett
4. A Systematic Analysis of Gene Functions by the Metabolic Pathway Database
Minoru Kanehisa and Susumu Goto
5. Polymer Dynamics of DNA, Chrornatin, and Chromosomes
Jörg Langowski, Lutz Ehrlich, Markus Hammermann, Christian Münkel, and Gero Wedemann
6. Is Whole Human Genome Sequencing Feasible?
Eugene W. Myers and James L. Weber
7. Sequence Pattems Diagnostic of Structure and Function
Temple F. Smith, R. Mark Adams, Sudeshna Das, Lihua Yu, Loredana Lo Conte, and James White
8. Recognizing Functional Domains in Biological Sequences
Gary D. Stormo
9. The Integrated Genomic Database (IGD)S: Enhancing the Productivity of Gene Mapping Projects
Stephen P. Bryant, Anastassia Spiridou, and Nigel K. Spurr
10. Error Analysis of Genetic Linkage Data
Robert Cottingham, Jr., Margaret Gelder Elm, and Marek Kimmel
11. Managing Accelerating Data Growth in the Genome Database
Kenneth H. Fasman
12. Advances in Statistical Methods for Linkage Analysis
Jeffrey R. O'Connell and Daniel E. Weeks
13. Exploring Heterogeneous Molecular Biology Databases in the Context of the Object-Protocol Model
Victor M. Markowitz, I.-Min A. Chen, and Anthony S. Kosky
14. Comprehensive Genome Information Systems
Otto Ritter
15. Visualizing the Genome
David B. Searls
16. Data Management for Ligand-Based Drug Design
Kari Aberer, Klemens Hemm, and Manfred Hendlich
17. Picturing the Working Protein
Hans Frauenfelder and Peter G. Wolynes
18. HIV- I Protease and Its Inhibitors
Maciej Geller, Joanna Trylska, and Jan Antosiewicz
19. Density Functional and Neural Network Analysis: Hydration Effects and Spectrosopic and Structural Correlations in Small Peptides and Arnino Acids
K. J. Jalkanen, S. Suhai, and H. Bohr
20. Computer Simulations of Protein-DNA Interactions
Mats Eriksson and Lennart Nilsson
21. The Role of Neutral MutatiOns in the Evolution of RNA Molecules
Peter Schuster
22. How Three-Fingered Snake Toxins Recognise Their Targets: Acetyicholinesterase-Fasciculin Complex, a Case Study
Kurt Giles, Mia L. Raves, Israel Silman, and Joel L. Sussman
23. Protein Sequence and Structure Comparison Using Iterative Double Dynamic Programming
William R. Taylor

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BIOMED Publications | 08.02.2000