This book represents the most comprehensive and up-to-date collection of information on the topic of computational molecular biology. Bringing the most recent research into the forefront of discussion, Algorithms in Computational Molecular Biology studies the most important and useful algorithms currently being used in the field, and provides related problems. It also succeeds where other titles have failed, in offering a wide range of information from the introductory fundamentals right up to the latest, most advanced levels of study.
Autorentext
Mourad Elloumi, PhD, is Associate Professor in Computer Science, Faculty of Economic Sciences and Management of Tunis (Tunisia), and member of the Unit of Technologies of Information and Communication (UTIC). He is the author/coauthor of more than forty publications in international journals and conferences. Professor Elloumi was the guest editor of a special issue on biological knowledge discovery and data mining in Knowledge-Based Systems and the coeditor of the proceedings of two international conferences.
Albert Y. Zomaya, PhD, is the Chair Professor of High Performance Computing and Networking in the School of Information Technologies at The University of Sydney (Australia). He is the author/coauthor of eight books and more than 400 publications in technical journals and conferences, and the editor of eight books and eight conference volumes. Professor Zomaya is currently an associate editor for twenty journals, the Founding Editor of the Wiley Series on Parallel and Distributed Computing, and a Founding Coeditor of the Wiley Series in Bioinformatics.
Inhalt
PREFACE xxxi
CONTRIBUTORS xxxiii
I STRINGS PROCESSING AND APPLICATION TO BIOLOGICAL SEQUENCES 1
1 STRING DATA STRUCTURES FOR COMPUTATIONAL MOLECULAR BIOLOGY 3
Christos Makris and Evangelos Theodoridis
2 EFFICIENT RESTRICTED-CASE ALGORITHMS FOR PROBLEMS IN COMPUTATIONAL BIOLOGY 27
Patricia A. Evans and H. Todd Wareham
3 FINITE AUTOMATA IN PATTERN MATCHING 51
Jan Holub
4 NEW DEVELOPMENTS IN PROCESSING OF DEGENERATE SEQUENCES 73
Pavlos Antoniou and Costas S. Iliopoulos
5 EXACT SEARCH ALGORITHMS FOR BIOLOGICAL SEQUENCES 91
Eric Rivals, Leena Salmela, and Jorma Tarhio
6 ALGORITHMIC ASPECTS OF ARC-ANNOTATED SEQUENCES 113
Guillaume Blin, Maxime Crochemore, and Stéphane Vialette
7 ALGORITHMIC ISSUES IN DNA BARCODING PROBLEMS 129
Bhaskar DasGupta, Ming-Yang Kao, and Ion Mandoiu
8 RECENT ADVANCES IN WEIGHTED DNA SEQUENCES 143
Manolis Christodoulakis and Costas S. Iliopoulos
9 DNA COMPUTING FOR SUBGRAPH ISOMORPHISM PROBLEM AND RELATED PROBLEMS 171
Sun-Yuan Hsieh, Chao-Wen Huang, and Hsin-Hung Chou
II ANALYSIS OF BIOLOGICAL SEQUENCES 191
10 GRAPHS IN BIOINFORMATICS 193
Elsa Chacko and Shoba Ranganathan
11 A FLEXIBLE DATA STORE FOR MANAGING BIOINFORMATICS DATA 221
Bassam A. Alqaralleh, Chen Wang, Bing Bing Zhou, and Albert Y. Zomaya
12 ALGORITHMS FOR THE ALIGNMENT OF BIOLOGICAL SEQUENCES 241
Ahmed Mokaddem and Mourad Elloumi
13 ALGORITHMS FOR LOCAL STRUCTURAL ALIGNMENT AND STRUCTURAL MOTIF IDENTIFICATION 261
Sanguthevar Rajasekaran, Vamsi Kundeti, and Martin Schiller
14 EVOLUTION OF THE CLUSTAL FAMILY OF MULTIPLE SEQUENCE ALIGNMENT PROGRAMS 277
Mohamed Radhouene Aniba and Julie Thompson
15 FILTERS AND SEEDS APPROACHES FOR FAST HOMOLOGY SEARCHES IN LARGE DATASETS 299
Nadia Pisanti, Mathieu Giraud, and Pierre Peterlongo
16 NOVEL COMBINATORIAL AND INFORMATION-THEORETIC ALIGNMENT-FREE DISTANCES FOR BIOLOGICAL DATA MINING 321
Chiara Epifanio, Alessandra Gabriele, Raffaele Giancarlo, and Marinella Sciortino
17 IN SILICO METHODS FOR THE ANALYSIS OF METABOLITES AND DRUG MOLECULES 361
Varun Khanna and Shoba Ranganathan
III MOTIF FINDING AND STRUCTURE PREDICTION 383
18 MOTIF FINDING ALGORITHMS IN BIOLOGICAL SEQUENCES 385
Tarek El Falah, Mourad Elloumi, and Thierry Lecroq
19 COMPUTATIONAL CHARACTERIZATION OF REGULATORY REGIONS 397
Enrique Blanco
20 ALGORITHMIC ISSUES IN THE ANALYSIS OF CHIP-SEQ DATA 425
Federico Zambelli and Giulio Pavesi
21 APPROACHES AND METHODS FOR OPERON PREDICTION BASED ON MACHINE LEARNING TECHNIQUES 449
Yan Wang, You Zhou, Chunguang Zhou, Shuqin Wang, Wei Du, Chen Zhang, and Yanchun Liang
22 PROTEIN FUNCTION PREDICTION WITH DATA-MINING TECHNIQUES 479
Xing-Ming Zhao and Luonan Chen
23 PROTEIN DOMAIN BOUNDARY PREDICTION 501
Paul D. Yoo, Bing Bing Zhou, and Albert Y. Zomaya
24 AN INTRODUCTION TO RNA STRUCTURE AND PSEUDOKNOT PREDICTION 521
Jana Sperschneider and Amitava Datta
IV PHYLOGENY RECONSTRUCTION 547
25 PHYLOGENETIC SEARCH ALGORITHMS FOR MAXIMUM LIKELIHOOD 549
Alexandros Stamatakis
26 HEURISTIC METHODS FOR PHYLOGENETIC RECONSTRUCTION WITH MAXIMUM PARSIMONY 579
Adrien Goëffon, Jean-Michel Richer, and Jin-Kao Hao
27 MAXIMUM ENTROPY METHOD FOR COMPOSITION VECTOR METHOD 599
Raymond H.-F. Chan, Roger W. Wang, and Jeff C.-F. Wong
V MICROARRAY DATA ANALYSIS 623
28 MICROARRAY GENE EXPRESSION DATA ANALYSIS 625
Alan Wee-Chung Liew and Xiangchao Gan
29 BICLUSTERING OF MICROARRAY DATA 651
Wassim Ayadi and Mourad Elloumi