Algorithmic Aspects of Bioinformatics

By: Hans-Joachim Böckenhauer , Dirk Bongartz

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Hardcover | 1 May 2007

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408 Pages

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23.39 x 15.6 x 2.39

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Advances in bioinformatics and systems biology require improved computational methods for analyzing data, while progress in molecular biology is in turn influencing the development of computer science methods. This book introduces some key problems in bioinformatics, discusses the models used to formally describe these problems, and analyzes the algorithmic approaches used to solve them.

After introducing the basics of molecular biology and algorithmics, Part I explains string algorithms and alignments; Part II details the field of physical mapping and DNA sequencing; and Part III examines the application of algorithmics to the analysis of biological data. Exciting application examples include predicting the spatial structure of proteins, and computing haplotypes from genotype data.

This book describes topics in detail and presents formal models in a mathematically precise, yet intuitive manner, with many figures and chapter summaries, detailed derivations, and examples. It is well suited as an introduction into the field of bioinformatics, and will benefit students and lecturers in bioinformatics and algorithmics, while also offering practitioners an update on current research topics.

Industry Reviews

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"This book is a worthy leader in what will surely be a torrent of high-level texts inspired by the success of DNA containing genetic instructions. ... this book is a highly recommended compendium of applications for geneticists and computer scientists. ... The computer science theory is developed in this text with ... numerous simple illustrations from DNA." (Harvey Cohn, ACM Computing Reviews, Vol. 49 (12), December, 2008)

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You Can Find This Book In

Non-Fiction Mathematics Algebra Computing & I.T.Computer Science Artificial Intelligence Computer Vision Science Biology, Life Sciences Life Sciences in General Genetics excluding Medical DNA & Genome

Biochemistry Computer Programming & Software Development Algorithms & Data Structures Mathematical Theory of Computation

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Paperback

Published: 30th November 2010

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Introduction	p. 1
Introduction and Basic Algorithms
Basics of Molecular Biology	p. 7
Proteins	p. 7
Nucleic Acids	p. 9
Hereditary Information and Protein Biosynthesis	p. 12
Experimental Techniques	p. 15
Basic Terms and Methods	p. 15
Duplication of DNA	p. 15
Gel Electrophoresis and Direct Sequencing	p. 16
DNA Chips	p. 19
Bibliographic Notes	p. 20
Basic Concepts: Strings, Graphs, and Algorithms	p. 23
Strings	p. 23
Graphs	p. 25
Algorithms and Complexity	p. 28
Bibliographic Notes	p. 35
String Algorithms	p. 37
The String Matching Problem	p. 37
String Matching Automata	p. 39
The Boyer-Moore Algorithm	p. 44
Suffix Trees	p. 50
Further Applications of Suffix Trees	p. 58
Generalized Suffix Trees and the Substring Problem	p. 58
Longest Common Substrings	p. 61
Efficient Computation of Overlaps	p. 63
Repeats in Strings	p. 66
Suffix Arrays	p. 68
Summary	p. 77
Bibliographic Notes	p. 78
Alignment Methods	p. 81
Alignment of Two Strings	p. 82
Basic Definitions	p. 82
Global Alignment	p. 84
Local and Semiglobal Alignment	p. 89
Generalized Scoring Functions	p. 94
Heuristic Methods for Database Search	p. 97
The FASTA Heuristic	p. 98
The BLAST Heuristic	p. 99
Multiple Alignments	p. 101
Definition and Scoring of Multiple Alignments	p. 101
Exact Computation of Multiple Alignments	p. 104
Combining Pairwise Alignments	p. 109
Summary	p. 114
Bibliographic Notes	p. 114
DNA Sequencing
Introduction and Overview	p. 119
Physical Mapping	p. 123
Restriction Site Mapping	p. 123
The Double Digest Approach	p. 124
The Partial Digest Approach	p. 131
Comparison of Methods for Restriction Site Mapping	p. 141
Hybridization Mapping	p. 143
Mapping with Unique Probes	p. 146
Mapping with Unique Probes and Errors	p. 157
Mapping with Non-unique Probes	p. 165
Summary	p. 166
Bibliographic Notes	p. 168
DNA Sequencing	p. 171
Shotgun Sequencing	p. 171
Crucial Points to Be Considered in a Suitable Model	p. 174
The Shortest Common Superstring Problem	p. 176
Refined Models for Fragment Assembly	p. 196
Sequencing by Hybridization	p. 201
Summary	p. 207
Bibliographic Notes	p. 208
Analyzing Biological Data
Finding Signals in DNA Sequences	p. 213
Identical and Similar Substrings	p. 213
Tandem Repeats	p. 217
Frequent and Infrequent Substrings	p. 223
Hidden Markov Models	p. 228
Summary	p. 235
Bibliographic Notes	p. 235
Genome Rearrangements	p. 237
Modeling	p. 237
Sorting Undirected Permutations	p. 239
Sorting Directed Permutations	p. 247
Computing the Syntenic Distance	p. 249
Summary	p. 255
Bibliographic Notes	p. 255
Phylogenetic Trees	p. 257
Ultrametric Distances	p. 258
Additive Trees	p. 265
Characters with Binary States	p. 268
The Parsimony Principle and the Quartet Method	p. 275
Summary	p. 283
Bibliographic Notes	p. 285
Haplotyping	p. 287
Inferring Haplotypes from a Population	p. 288
Haplotyping a Single Individual	p. 305
Summary	p. 316
Bibliographic Notes	p. 316
Molecular Structures	p. 319
RNA Secondary Structure Prediction	p. 320
Minimizing the Free Energy	p. 322
Stochastic Context-Free Grammars	p. 329
Structure-Based Comparison of Biomolecules	p. 337
Protein Structure Prediction	p. 349
De Novo Structure Prediction - The HP Model	p. 352
Protein Threading	p. 363
Summary	p. 369
RNA Secondary Structure Prediction	p. 369
Structure-Based Comparison of Biomolecules	p. 371
Protein Structure Prediction	p. 371
Bibliographic Notes	p. 372
RNA Secondary Structure Prediction	p. 372
Structure-Based Comparison of Biomolecules	p. 373
Protein Structure Prediction	p. 374
References	p. 377
Index	p. 389
Table of Contents provided by Ingram. All Rights Reserved.

Algorithmic Aspects of Bioinformatics

At a Glance

Hardcover

Industry Reviews

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How to return your order

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You Can Find This Book In

Other Editions and Formats

Paperback

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