Compact handbook of computational biology

570 Pages·2004·11.93 MB·English

by  Andrzej K. Konopka

COMPACT HANDBOOK OF
Computational
Biology
Edited by
Andrzej K.Konopka
M.James C.Crabbe
MARCEL DEKKER NEW YORK
Copyright © 2004 by Marcel Dekker
Although great care has been taken to provide accurate and current information, neither
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ISBN: 0-8247-0982-9
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Copyright © 2004 by Marcel Dekker
Foreword
Computational biology is a relatively new but already mature field of academic
research. In this handbook we focused on the following three goals:
1. Outlining pivotal general methodologies that will guide research for
the years to come.
2. Providing a survey of specific algorithms, which have been successfully
applied in molecular biology, genomics, structural biology and
bioinformatics.
3. Describing and explaining away multiple misconceptions that could
jeopardize science and software development of the future.
The handbook is written for mature readers with a great deal of rigorous
experience with either doing scientific research or writing scientific software.
However no specific background in computer science, statistics, or biology is
required to understand most of the chapters. In order to accommodate the
readers who wish to become professional computational biologists in the
future we also provide appendices that contain educationally sound glossaries
of terms and descriptions of major sequence analysis algorithms. This can
also be of help to executives in charge of industrial bioinformatics as well as
to academic teachers who plan their courses in bioinformatics, computational
biology, or one of the “*omics” (genomics, proteomics, and their variants).
As a matter of fact we believe that this volume should be suitable as a senior
undergraduate or graduate-level textbook of computational biology within
departments that pertain to any of the life sciences. Selected chapters could
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Copyright © 2004 by Marcel Dekker
iv Foreword
also be used as teaching materials for students of computer science and
bioengineering.
This handbook is a true celebration of computational biology. It has been
in preparation for a very long time with multiple updates and exchanges of
chapters. However the quality and potential usefulness of the contributions
make us believe that preparing the ultimate final version was the time very
well spent.
Our thanks go to all the authors for their masterful contributions and
devotion to the mission of science. We would also like to extend our most
sincere thanks to our publishing editor Anita Lekhwani and the outstanding
production editor Barbara Methieu. Their almost infinite patience and
encouragement during inordinately long periods of collecting updates and
final versions of the chapters greatly contributed to timely completion of this
project.
Andrzej K.Konopka and M.James C.Crabbe
Copyright © 2004 by Marcel Dekker
Contents
Foreword iii
Contributors vii

1. Introduction: Computational Biology in 14 Brief Paragraphs 1
Andrzej K.Konopka and M.James C.Crabbe

Part I. Biomolecular Sequence Analysis

2. Introduction to Pragmatic Analysis of Nucleic Acid Sequences 7
Andrzej K.Konopka
3. Motifs in Sequences: Localization and Extraction 47
Maxime Crochemore and Marie-France Sagot
4. Protein Sequence Analysis and Prediction of Secondary 99
Structural Features
Jaap Heringa

Part II. Biopolymer Structure Calculation and Prediction

5. Discrete Models of Biopolymers 187
Peter Schuster and Peter F.Stadler
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Copyright © 2004 by Marcel Dekker
vi Contents
6. Protein Structure Folding and Prediction 223
William R.Taylor
7. DNA-Protein Interactions: Target Prediction 241
Akinori Sarai and Hidetoshi Kono

Part III. Genome Analysis and Evolution

8. Methods of Computational Genomics: An Overview 279
Frederique Lisacek
9. Computational Aspects of Comparative Genomics 343
Wojciech Makalowski and Izabela Makalowska
10. Computational Methods for Studying the Evolution
of the Mitochondrial Genome 369
Cecilia Saccone and Graziano Pesole

Appendix 1: Computational Biology: Annotated Glossary of Terms 451
Compiled by Andrzej K.Konopka, Philipp Bucher, M.James
C.Crabbe, Maxim Crochemore, Jaap Heringa, Frederique
Lisacek, Izabela Makalowska, Wojciech Makalowski,
Graziano Pesole, Cecilia Saccone, Marie-France Sagot,
Akinori Sarai, Peter Stadler, and William R.Taylor
Appendix 2: A Dictionary of Programs for Sequence Analysis 503
Andrzej K.Konopka and Jaap Heringa
Copyright © 2004 by Marcel Dekker
Contributors
Philipp Bucher Bioinformatics, Institut Suisse de Recherches Experimentales
sur le Cancer (ISREC), Epalinges s/Lausanne, Switzerland
M.James C.Crabbe University of Reading, Whiteknights, Reading, England
Maxime Crochemore Institut Gaspard-Monge, University of Marne-la-Vallée,
Marne-la-Vallée, France
Jaap Heringa Centre for Integrative Bioinformatics VU (IBIYU), Faculty of
Sciences and Faculty of Earth and Life Sciences, Free University, Amsterdam,
The Netherlands, and MRC National Institute for Medical Research, London,
England
Hidetoshi Kono University of Pennsylvania, Philadelphia, Pennsylvania,
U.S.A.
Andrzej K.Konopka BioLingua Research Inc., Gaithersburg, Maryland, U.S.A.
Frederique Lisacek Génome and Informatique, Evry, France and Geneva
Bionformatics (GeneBio), Geneva, Switzerland
Izabela Makalowska Pennsylvania State University, University Park, PA,
U.S.A.
vii
Copyright © 2004 by Marcel Dekker
viii Contributors
Wojciech Makalowski Pennsylvania State University, University Park, PA,
U.S.A.
Graziano Pesole University of Milan, Milan, Italy
Cecilia Saccone University of Bari, Bari, Italy
Marie-France Sagot INRIA, Laboratoire de Biométrie et Biologie Évolutive,
University Claude Bernard, Lyon, France
Akinori Sarai RIKEN Institute, Tsukuba Life Science Center, Tsukuba, Japan
Peter Schuster University of Vienna, Vienna, Austria
Peter F.Stadler University of Leipzig, Leipzig, Germany
William R.Taylor National Institute for Medical Research, London, England
Copyright © 2004 by Marcel Dekker
1
Introduction: Computational Biology
in 14 Brief Paragraphs
Andrzej K.Konopka
BioLingua Research Inc., Gaithersburg, Maryland, U.S.A.
M.James C.Crabbe
University of Reading, Whiteknights, Reading, England
1. Computational biology has been a marvelous experience for at least three
generations of the brightest scientists of the second half of the twentieth
century and continues to be so in the twenty-first century. Simply speaking,
computational biology is the science of biology done with the use of
computers. Because computers require some specialized knowledge of the
cultural and technical infrastructure in which they can be used, computational
biology is significantly motivated (or even inspired) by computer science and
its engineering variant known as information technology. On the other hand,
the kind of data and data structures that can be processed by computers
provide practical constraints on the selection of computational biology
research topics. For instance, it is easier to analyze sequences of biopolymers
with string processing techniques and statistics than to infer unknown
biological functions from the unknown three-dimensional structures of the
same biopolymers by using image processing tools. Similarly, it is advisable to
1
Copyright © 2004 by Marcel Dekker