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This volume features highlights from the DIMACS Special Year on "Mathematical Support for Molecular Biology". Top researchers presented both new research results and comprehensive overviews on the use of mathematics (especially discrete mathematics) and theoretical computer science in molecular biology. The book provides a unique "snapshot" of this growing area of study. It will be of interest to both experts and novices seeking information on the state of the research.
Foreword vii Preface ix An introduction to molecular biology for mathematicians and computer programmers W. M. Fitch 1 New uses for uniform lifted alignments D. Gusfield and L. Wang 33 Sequence alignment and phylogeny construction M. Vingron 53 A new look at tree models for multiple sequence alignment D. Durand 65 Sequence alignment in molecular biology A. Apostolico and R. Giancarlo 85 Formal language theory and biological macromolecules D. B. Searls 117 Global optimization approaches in protein folding and peptide docking C. A. Floudas, J. L. Klepeis, and P. M. Pardalos 141 The topologically driven strand separation transition in DNA---methods of analysis and biological significance C. J. Benham 173 Parallel strategies for DNA manipulation and analysis C. L. Smith, T. Sano, N. E. Broude, and C. R. Cantor 199 A column-generation based branch-and-bound algorithm for sorting by reversals A. Caprara, G. Lancia, and S.-K. Ng 213 Visualizing measures of genetic distance E. M. Jordan 227 Fragment assembly system for DNA sequencing projects L. Milanesi, M. Marsilli, G. Mauri, C. Rolfi, and L. Uboldi 241 Performance of the CAP2 sequence assembly program X. Huang 259 A simple toolkit for DNA fragment assembly J. Meidanis 271