Algorithmic Aspects of Bioinformatics
Advances in bioinformatics and systems biology require improved computational methods for analyzing data, while progress in molecular biology is in turn influencing the development of computer science methods. This book introduces some key problems in bio
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Advisory Board: S. Amari G. Brassard K.A. De Jong C.C.A.M. Gielen T. Head L. Kari L. Landweber T. Martinetz Z. Michalewicz M.C. Mozer E. Oja G. P˘aun J. Reif H. Rubin A. Salomaa M. Schoenauer H.-P. Schwefel C. Torras D. Whitley E. Winfree J.M. Zurada
Hans-Joachim Böckenhauer Dirk Bongartz
Algorithmic Aspects of Bioinformatics
With 118 Figures and 9 Tables
123
Authors
Series Editors
Dr. Hans-Joachim Böckenhauer ETH Zurich Information Technology and Education CAB F11 Universitätsstr. 6 8092 Zurich Switzerland [email protected]
G. Rozenberg (Managing Editor) [email protected]
Dr. Dirk Bongartz Computer Science I RWTH Aachen Germany [email protected]
A.E. Eiben Vrije Universiteit Amsterdam The Netherlands
Th. Bäck, J.N. Kok, H.P. Spaink Leiden Center for Natural Computing Leiden University Niels Bohrweg 1 2333 CA Leiden, The Netherlands
Library of Congress Control Number: 2007924247
ACM Computing Classification (1998): F.2.2, G.2.1, G.2.2, J.3 ISSN 1619-7127 ISBN 978-3-540-71912-0 Springer Berlin Heidelberg New York This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilm or in any other way, and storage in data banks. Duplication of this publication or parts thereof is permitted only under the provisions of the German Copyright Law of September 9, 1965, in its current version, and permission for use must always be obtained from Springer. Violations are liable for prosecution under the German Copyright Law. Springer is a part of Springer Science+Business Media springer.com © Springer-Verlag Berlin Heidelberg 2007 Originally published in the German language by B.G. Teubner Verlag as “Hans-Joachim Böckenhauer und Dirk Bongartz: Algorithmische Grundlagen der Bioinformatik”. © B.G. Teubner Verlag | GWV Fachverlage GmbH, Wiesbaden 2003 The use of general descriptive names, registered names, trademarks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. Cover Design: KünkelLopka, Werbeagentur, Heidelberg Typesetting: by the Authors Production: LE-TEX Jelonek, Schmidt & Vöckler GbR, Leipzig Printed on acid-free paper
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Preface
The discovery of the double-helix structure of DNA by Watson and Crick more than fifty years ago was the starting point of a new era in molecular biology. Since then, our knowledge of biological structures and processes has grown tremendously. But many of these advances would have been unthinkable without using computational methods. Computer science plays a leading role in the emerging interdisciplinary field of bioinformatics. Only the interplay between biological methods and concepts from informatics has enabled us to successfully maintain projects such as the Human Genome Project. But completing this project also initiated further ch
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