Compact Handbook of Computational Biology

Andrzej K. Konopka , BioLingua Research, Inc., Gaithersburg, Maryland, U.S.A. M. James C. Crabbe , University of Reading, Reading, United Kingdom As computational methods continue to extend the reach of traditional study designs in biological research, this interdisciplinary handbook emerges as the first of its scale and caliber to synthesize foundational concepts, techniques, and challenges distinctive to biomolecular sequence analysis, biopolymer structure analysis and prediction, and genomic analysis and evolution-presenting authoritative descriptions backed by over 975 works cited as well as practical guidelines direct from more than one dozen field luminaries. Table of Contents BIOMOLECULAR SEQUENCE ANALYSIS Motifs in Sequences: Localization and Extraction M. Crochemore and M.-F. Sagot Nucleic Acid Sequence Analysis A. K. Konopka Protein Sequence Analysis and Prediction of Secondary Structural Features J. Heringa Profile Analysis and Hidden Markov Models P. Bucher BIOPOLYMER STRUCTURE CALCULATION AND PREDICTION Discrete Models of Biopolymers P. Schuster and P. Stadler Protein Structure Folding and Prediction W. R. Taylor DNA-Protein Interactions: Target Prediction A. Sarai and H. Kono GENOME ANALYSIS AND EVOLUTION Computational Genomics: An Overview F. Lisacek Computational Aspects of Comparative Genomics W. Makalowski and I. Makalowska Computational Methods for Studying the Evolution of Mitochondrial Genome C. Saccone and G. Pesole Appendix 1: Computational Biology and Bioinformatics: Annotated Guide to Literature A. K. Konopka and M. J. C. Crabbe Appendix 2: Computational Biology and Bioinformatics: Annotated Glossary of Terms A .K. Konopka, M .J. C. Crabbe, P. Bucher, M. Crochemore, J. Heringa, H. Kono, F. Lisacek, W. Makalowski, I. Makalowska, G. Pesole, C. Saccone, M.-F. Sagot, A. Sarai, P. Schuster, P. Stadler, and W. R. Taylor Appendix 3: Computational Biology and Bioinformatics: Annotated Guide to Software, Databases, and Internet Resources A. K. Konopka, M. J. C. Crabbe, P. Bucher, M. Crochemore, J. Heringa, H. Kono, F. Lisacek, W. Makalowski, I. Makalowska, G. Pesole, C. Saccone, M.-F. Sagot, A. Sarai, P. Schuster, P. Stadler, and W.R. Taylor