Computational Molecular Biology: An Introduction / Edition 1

Computational Molecular Biology: An Introduction / Edition 1

by Peter Clote, Rolf Backofen
     
 

ISBN-10: 0471872512

ISBN-13: 9780471872511

Pub. Date: 10/11/2000

Publisher: Wiley

Recently molecular biology has undergone unprecedented development generating vast quantities of data needing sophisticated computational methods for analysis, processing and archiving. This requirement has given birth to the truly interdisciplinary field of computational biology, or bioinformatics, a subject reliant on both theoretical and practical contributions…  See more details below

Overview

Recently molecular biology has undergone unprecedented development generating vast quantities of data needing sophisticated computational methods for analysis, processing and archiving. This requirement has given birth to the truly interdisciplinary field of computational biology, or bioinformatics, a subject reliant on both theoretical and practical contributions from statistics, mathematics, computer science and biology.
* Provides the background mathematics required to understand why certain algorithms work
* Guides the reader through probability theory, entropy and combinatorial optimization
* In-depth coverage of molecular biology and protein structure prediction
* Includes several less familiar algorithms such as DNA segmentation, quartet puzzling and DNA strand separation prediction
* Includes class tested exercises useful for self study
* Source code of programs available on a Web site Primarily aimed at advanced undergraduate and graduate students from bioinformatics, computer science, statistics, mathematics and the biological sciences, this text will also interest researchers from these fields.

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Product Details

ISBN-13:
9780471872511
Publisher:
Wiley
Publication date:
10/11/2000
Series:
Wiley Series in Mathematical & Computational Biology Series, #1
Pages:
300
Product dimensions:
6.81(w) x 10.04(h) x 0.91(d)

Table of Contents

Series Preface
Preface
1Molecular Biology1
1.1Some Organic Chemistry3
1.2Small Molecules4
1.3Sugars6
1.4Nucleic Acids6
1.5Proteins14
1.6From DNA to Proteins17
1.7Exercises21
2Math Primer23
2.1Probability23
2.2Combinatorial Optimization53
2.3Entropy and Applications to Molecular Biology61
2.4Exercises72
2.5Appendix: Modification of Bezout's Lemma77
3Sequence Alignment81
3.1Motivating Example83
3.2Scoring Matrices84
3.3Global Pairwise Sequence Alignment88
3.4Multiple Sequence Alignment111
3.5Genomic Rearrangements118
3.6Locating Cryptogenes and Guide RNA120
3.7Expected Length of gRNA in Trypanosomes123
3.8Exercises128
3.9Appendix: Maximum-Likelihood Estimation for Pair Probabilities132
4All About Eve135
4.1Introduction135
4.2Rate of Evolutionary Change137
4.3Clustering Methods144
4.4Maximum Likelihood157
4.5Quartet Puzzling166
4.6Exercises171
5Hidden Markov Models175
5.1Likelihood and Scoring a Model177
5.2Re-estimation of Parameters180
5.3Applications193
5.4Exercises197
6Structure Prediction201
6.1RNA Secondary Structure202
6.2DNA Strand Separation213
6.3Amino Acid Pair Potentials223
6.4Lattice Models of Proteins228
6.5Hart and Istrial's Approximation Algorithm234
6.6Constraint-Based Structure Prediction243
6.7Protein Threading246
6.8Exercises259
App. A Mathematical Background263
App. B Resources265
References269
Index281

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