Algorithms in Computational Molecular Biology

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.

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 Stphane 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 Goffon, 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 30 COMPUTATIONAL MODELS FOR CONDITION-SPECIFIC GENE AND PATHWAY INFERENCE 665 Yu-Qing Qiu, Shihua Zhang, Xiang-Sun Zhang, and Luonan Chen 31 HETEROGENEITY OF DIFFERENTIAL EXPRESSION IN CANCER STUDIES: ALGORITHMS AND METHODS 691 Radha Krishna Murthy Karuturi VI ANALYSIS OF GENOMES 723 32 COMPARATIVE GENOMICS: ALGORITHMS AND APPLICATIONS 725 Xiao Yang and Srinivas Aluru 33 ADVANCES IN GENOME REARRANGEMENT ALGORITHMS 749 Masud Hasan and M. Sohel Rahman 34 COMPUTING GENOMIC DISTANCES: AN ALGORITHMIC VIEWPOINT 773 Guillaume Fertin and Irena Ru