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Biomolecular sequence comparison is the origin of bioinformatics. This book gives a complete in-depth treatment of the study of sequence comparison. A comprehensive introduction is followed by a focus on alignment algorithms and techniques, proceeded by a discussion of the theory. The book examines alignment methods and techniques, features a new issue of sequence comparison - the spaced seed technique, addresses several new flexible strategies for coping with various scoring schemes, and covers the theory on the significance of high-scoring segment pairs between two unalignment sequences. Useful appendices on basic concepts in molecular biology, primer in statistics and software for sequence alignment are included in this reader-friendly text, as well as chapter-ending exercise and research questions A state-of-the-art study of sequence alignment and homology search, this is an ideal reference for advanced students studying bioinformatics and will appeal to biologists who wish to know how to use homology search tools.

For Comparison

Until a few years ago I concentrated my attention on workers' compensa­ tion programs in the United States and Canada. Because the United States has 52 programs and Canada has eight, I was exposed to a diversity of approaches that caused me to believe that few other approaches existed. Since 1984 I have become more aware of what the rest of the world has been doing and discovered that my knowledge needed to be broadened significantly. The trigger action was a 1984 faculty research exchange agreement between Keio University in Tokyo and the University of Minnesota that made it possible for me to spend much of my time studying Japan's workers' compensation program and comparing it with the United States approaches. Japan's program had several features that I had not encountered in the United States or Canada. After this experience I attached considerably more value to and spent more time studying the Social Security Administration's biennial reports on Social Security Pro­ grams Throughout The World, which include workers' compensation programs. I also presented papers at two meetings of the International Insurance Society based on my Japanese and Social Security Adminis­ tration report research. Many participants urged further study in this area and offered to send me materials describing their nations' programs. The result is this study which I hope that readers will find interesting and worthwhile.

LÉNA SOLER This volume is a collection of essays devoted to the analysis of scientific change and stability. It represents the most recent thinking on the topic of incommensurability and scientific theory change. It explores the balance and tension that exists between commensurability and continuity (or stabilities) on the one hand, and incommen- rability and discontinuity (or ruptures) on the other. And it discusses some central epistemological consequences regarding the nature of scientific progress, rationality and realism. With respect to these topics, it investigates a number of new avenues and revisits some familiar issues, with a focus on the history and philosophy of physics, in a way that is informed by developments in cognitive sciences as well as the claims of “New experimentalists”. The essays in this book are fully revised versions of papers which were ori- nally presented at the international colloquium, “Repenser l’Ãvaluation comparative des thÃories scientifiques: stabilitÃs, ruptures, incommensurabilitÃs?” organized by LÃna Soler and Paul Hoyningen-Huene at the University of Nancy, France, in June 2004. Each paper is followed by a critical comment, which either represents an opposing viewpoint or suggests some developments. The conference was a striking example of the sort of genuine dialogue that can take place between philosophers of science, historians of science and scientists who come from different traditions and endorse opposing commitments. I hope that this is evident in the book too and that it will constitute one of its attractions.

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