Problems and Solutions in Biological Sequence Analysis

ISBN-10: 0521612306
ISBN-13: 9780521612302
Edition: 2006
List price: $67.00 Buy it from $55.38
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Description: Biological Sequence Analysis (BSA) by Durbin et al. has been widely adopted as a required text for bioinformatics courses at leading universities world-wide. The problems included in BSA as exercises for readers have been repeatedly used by  More...

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Book details

List price: $67.00
Copyright year: 2006
Publisher: Cambridge University Press
Publication date: 9/11/2006
Binding: Paperback
Pages: 360
Size: 6.75" wide x 9.25" long x 0.75" tall
Weight: 1.584
Language: English

Biological Sequence Analysis (BSA) by Durbin et al. has been widely adopted as a required text for bioinformatics courses at leading universities world-wide. The problems included in BSA as exercises for readers have been repeatedly used by instructors for homework and tests. However, instructors had frequently expressed a need for fully worked solutions and an additional collection of problems with accompanying solutions. This book provides just that: following the same structure as BSA, it will facilitate a better understanding of the contents of the BSA chapters and will enable readers to develop the problem solving skills vitally important for conducting successful research in the field of bioinformatics. All of the material has been class-tested by the authors at Georgia Tech, where the first ever MSc degree programme in Bioinformatics was held.

Mark Borodovsky is the Regents' Professor of Biology and Biomedical Engineering and Director of the Center for Bioinformatics and Computational Biology at Georgia Institute of Technology in Atlanta. He is the founder of the Georgia Tech M.Sc. and Ph.D. degree programs in Bioinformatics. His research interests are in bioinformatics and systems biology. He has taught Bioinformatics courses since 1994.

Svetlana Ekisheva is a Research Scientist at the School of Biology, Georgia Institute of Technology, Atlanta. Her research interests are in bioinformatics, applied statistics and stochastic processes. Her expertise includes teaching probability theory and statistics at universities in Russia and in the USA.

Preface
Introduction
Original problems
Additional problems
Further reading
Pairwise alignment
Original problems
Additional problems and theory
Derivation of the amino acid substitution matrices (PAM series)
Distributions of similarity scores
Distribution of the length of the longest common word among several unrelated sequences
Further reading
Markov chains and hidden Markov models
Original problems
Additional problems and theory
Probabilistic models for sequences of symbols: selection of the model and parameter estimation
Bayesian approach to sequence composition analysis: the segmentation model by Liu and Lawrence
Further reading
Pairwise alignment using HMMs
Original problems
Additional problems
Further reading
Profile HMMs for sequence families
Original problems
Additional problems and theory
Discrimination function and maximum discrimination weights
Further reading
Multiple sequence alignment methods
Original problem
Additional problems and theory
Carrillo-Lipman multiple alignment algorithm
Progressive alignments: the Feng-Doolittle algorithm
Gibbs sampling algorithm for local multiple alignment
Further reading
Building phylogenetic trees
Original problems
Additional problems
Further reading
Probabilistic approaches to phylogeny
Original problems
Bayesian approach to finding the optimal tree and the Mau-Newton-Larget algorithm
Additional problems and theory
Relationship between sequence evolution models described by the Markov and the Poisson processes
Thorne-Kishino-Felsenstein model of sequence evolution with substitutions, insertions, and deletions
More on the rates of substitution
Further reading
Transformational grammars
Original problems
Further reading
RNA structure analysis
Original problems
Further reading
Background on probability
Original problems
Additional problem
Further reading
References
Index

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