Problems and Solutions in Biological Sequence Analysis

A companion to Biological Sequence Analysis (Cambridge, 1998), providing solutions to the original problems and additional worked examples.

Mark Borodovsky (Author), Svetlana Ekisheva (Author)

9780521847544, Cambridge University Press

Hardback, published 4 September 2006

366 pages, 27 b/w illus. 27 tables 172 exercises
25.6 x 17.7 x 2.2 cm, 0.867 kg

This book is the first of its kind to provide a large collection of bioinformatics problems with accompanying solutions. Notably, the problem set includes all of the problems offered in Biological Sequence Analysis, by Durbin et al. (Cambridge, 1998), widely adopted as a required text for bioinformatics courses at leading universities worldwide. Although many of the problems included in Biological Sequence Analysis as exercises for its readers have been repeatedly used for homework and tests, no detailed solutions for the problems were available. Bioinformatics instructors had therefore frequently expressed a need for fully worked solutions and a larger set of problems for use on courses. This book provides just that: following the same structure as Biological Sequence Analysis and significantly extending the set of workable problems, it will facilitate a better understanding of the contents of the chapters in BSA and will help its readers develop problem-solving skills that are vitally important for conducting successful research in the growing field of bioinformatics. All of the material has been class-tested by the authors at Georgia Tech, where the first ever MSc degree program in Bioinformatics was held.

Preface
1. Introduction
2. Pairwise alignment
3. Markov chains and hidden Markov models
4. Pairwise alignment using HMMs
5. Profile HMMs for sequence families
6. Multiple sequence alignment methods
7. Building phylogenetic trees
8. Probabilistic approaches to phylogeny
9. Transformational grammars
10. RNA structure analysis
11. Background on probability.

Subject Areas: Data mining [UNF], 3D graphics & modelling [UGK], Biotechnology [TCB], Genetics [non-medical PSAK]