DIMACS Series in
Discrete Mathematics and Theoretical Computer Science

VOLUME Forty Seven
TITLE: "Mathematical Support for Molecular Biology"
EDITORS: Martin Farach-Colton, Fred S. Roberts, Martin Vingron and Michael Waterman

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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

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Document last modified on October 28, 1998.