Introduction to Mathematical Methods in Bioinformatics / created by Alexander Isaev

Includes bibliographical references and index

Sequence Analysis Introduction: Biological Sequences Sequence Alignment Markov Chains and Hidden Markov Models Protein Folding Phylogenetic Reconstruction Mathematical Background for Sequence Analysis Elements of Probability Theory Significance of Sequence Alignment Scores Elements of Statistics Substitution Matrices

ToMathematical Methodsin Bioinformatics With 76 Figures and 3 Tables Alexander Isaev Australian National University Department of Mathematics Canberra, ACT 0200 Australia e-mail: alexander. isaev@maths. anu. edu. au Corrected Second Printing 2006 Mathematics Subject Classi?cation (2000 ): 91 -01 (Primary) 91 D20 (Secondary) Libraryof Congress Control Number: 2006930998 ISBN: 3-540 -21973 -0 ISBN: 9783540219736 This work is subject to copyright. All rights are reserved, whether the whole or part of the mat- ial is concerned, speci?cally the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on micro?lm or in any other way, and storage in data banks. Dup- cation 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 beobtainedfromSpringer. ViolationsareliableforprosecutionundertheGermanCopyrightLaw. Springer is a part of Springer Science+Business Media springer. com Springer-Verlag Berlin Heidelberg 2006 The use of general descriptive names, registered names, trademarks, etc. in this publication does not imply, even in the absence of a speci?c statement, that such names are exempt from the re- vant protective laws and regulations and therefore free for general use. Cover design: Erich Kirchner, Heidelberg A Typesetting by the author and SPi using a Springer LT X macro package E Printed on acid-free paper: SPIN:11809142 41 /2141 /SPi-543210 To Esya and Masha Preface Broadly speaking, Bioinformatics can be de?ned as a collection of mathema- cal, statistical and computational methods for analyzing biological sequences, thatis,DNA,RNAandaminoacid(protein)sequences