Essential Bioinformatics

By: Jin Xiong

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Paperback | 1 June 2008

At a Glance

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339 Pages

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25.4 x 17.78 x 1.91

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Essential Bioinformatics is a concise yet comprehensive textbook of bioinformatics, which provides a broad introduction to the entire field. Written specifically for a life science audience, the basics of bioinformatics are explained, followed by discussions of the state-of-the-art computational tools available to solve biological research problems.

All key areas of bioinformatics are covered including biological databases, sequence alignment, genes and promoter prediction, molecular phylogenetics, structural bioinformatics, genomics and proteomics. The book emphasizes how computational methods work and compares the strengths and weaknesses of different methods.

This balanced yet easily accessible text will be invaluable to students who do not have sophisticated computational backgrounds. Technical details of computational algorithms are explained with a minimum use of mathematical formulae; graphical illustrations are used in their place to aid understanding.

The effective synthesis of existing literature as well as in-depth and up-to-date coverage of all key topics in bioinformatics make this an ideal textbook for all bioinformatics courses taken by life science students and for researchers wishing to develop their knowledge of bioinformatics to facilitate their own research.

Concise yet comprehensive and written specifically for life scientists and those without a sophisticated computational background
Provides annotated guides to the most frequently used internet tools for each topic and discusses the advantages of different methods
Includes 6 step-by-step protocols for internet-based exercises to aid student's problem-solving skills using freely available bioinformatics tools
Glossary provides clear definitions and easy understanding of key bioinformatics concepts and tools.

About the Author

Jin Xiong is Assistant Professor of Biology at Texas A & M University, where he has taught bioinformatics to graduate and undergraduate students for several years.

Industry Reviews

'Essential Bioinformatics is a welcome addition to this area, by having a broad general approach that I think is particularly suitable for undergraduate teaching. The advantage of this being a new book is that there is not an overriding focus on structural bioinformatics that was seen in some earlier texts, which allows for a much broader coverage of newer areas like comparative and functional genomics.' http://www.sgm.ac.uk/pubs/micro_today/book_reviews/MTNOV06/MTN06_31.cfm 'The book would be ideal for biologists who wish to gain a grasp of the different analysis techniques available to the microarray user.' http://www.sgm.ac.uk/pubs/micro_today/book_reviews/MTAUG04/MTA04_13.cfm 'Awareness of bioinformatics is essential in a modern microbiological qualification and as this subject matures there are an increasing number of texts available. Essential Bioinformatics is a welcome addition to this area, by having a broad general approach that I think is particularly suitable for the undergraduate teaching.' Gavin Thomas, University of York

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Non-Fiction Science Biology, Life Sciences Life Sciences in General Genetics excluding Medical Computing & I.T.Information Technology General Issue

Preface	p. ix
Introduction and Biological Databases
Introduction	p. 3
What Is Bioinformatics?	p. 4
Goal	p. 5
Scope	p. 5
Applications	p. 6
Limitations	p. 7
New Themes	p. 8
Further Reading	p. 8
Introduction to Biological Databases	p. 10
What Is a Database?	p. 10
Types of Databases	p. 10
Biological Databases	p. 13
Pitfalls of Biological Databases	p. 17
Information Retrieval from Biological Databases	p. 18
Summary	p. 27
Further Reading	p. 27
Sequence Alignment
Pairwise Sequence Alignment	p. 31
Evolutionary Basis	p. 31
Sequence Homology versus Sequence Similarity	p. 32
Sequence Similarity versus Sequence Identity	p. 33
Methods	p. 34
Scoring Matrices	p. 41
Statistical Significance of Sequence Alignment	p. 47
Summary	p. 48
Further Reading	p. 49
Database Similarity Searching	p. 51
Unique Requirements of Database Searching	p. 51
Heuristic Database Searching	p. 52
Basic Local Alignment Search Tool (BLAST)	p. 52
FASTA	p. 57
Comparison of FASTA and BLAST	p. 60
Database Searching with the Smith-Waterman Method	p. 61
Summary	p. 61
Further Reading	p. 62
Multiple Sequence Alignment	p. 63
Scoring Function	p. 63
Exhaustive Algorithms	p. 64
Heuristic Algorithms	p. 65
Practical Issues	p. 71
Summary	p. 73
Further Reading	p. 74
Profiles and Hidden Markov Models	p. 75
Position-Specific Scoring Matrices	p. 75
Profiles	p. 77
Markov Model and Hidden Markov Model	p. 79
Summary	p. 84
Further Reading	p. 84
Protein Motifs and Domain Prediction	p. 85
Identification of Motifs and Domains in Multiple Sequence Alignment	p. 86
Motif and Domain Databases Using Regular Expressions	p. 86
Motif and Domain Databases Using Statistical Models	p. 87
Protein Family Databases	p. 90
Motif Discovery in Unaligned Sequences	p. 91
Sequence Logos	p. 92
Summary	p. 93
Further Reading	p. 94
Gene and Promoter Prediction
Gene Prediction	p. 97
Categories of Gene Prediction Programs	p. 97
Gene Prediction in Prokaryotes	p. 98
Gene Prediction in Eukaryotes	p. 103
Summary	p. 111
Further Reading	p. 111
Promoter and Regulatory Element Prediction	p. 113
Promoter and Regulatory Elements in Prokaryotes	p. 113
Promoter and Regulatory Elements in Eukaryotes	p. 114
Prediction Algorithms	p. 115
Summary	p. 123
Further Reading	p. 124
Molecular Phylogenetics
Phylogenetics Basics	p. 127
Molecular Evolution and Molecular Phylogenetics	p. 127
Terminology	p. 128
Gene Phylogeny versus Species Phylogeny	p. 130
Forms of Tree Representation	p. 131
Why Finding a True Tree Is Difficult	p. 132
Procedure	p. 133
Summary	p. 140
Further Reading	p. 141
Phylogenetic Tree Construction Methods and Programs	p. 142
Distance-Based Methods	p. 142
Character-Based Methods	p. 150
Phylogenetic Tree Evaluation	p. 163
Phylogenetic Programs	p. 167
Summary	p. 168
Further Reading	p. 169
Structural Bioinformatics
Protein Structure Basics	p. 173
Amino Acids	p. 173
Peptide Formation	p. 174
Dihedral Angles	p. 175
Hierarchy	p. 176
Secondary Structures	p. 178
Tertiary Structures	p. 180
Determination of Protein Three-Dimensional Structure	p. 181
Protein Structure Database	p. 182
Summary	p. 185
Further Reading	p. 186
Protein Structure Visualization, Comparison, and Classification	p. 187
Protein Structural Visualization	p. 187
Protein Structure Comparison	p. 190
Protein Structure Classification	p. 195
Summary	p. 199
Further Reading	p. 199
Protein Secondary Structure Prediction	p. 200
Secondary Structure Prediction for Globular Proteins	p. 201
Secondary Structure Prediction for Transmembrane Proteins	p. 208
Coiled Coil Prediction	p. 211
Summary	p. 212
Further Reading	p. 213
Protein Tertiary Structure Prediction	p. 214
Methods	p. 215
Homology Modeling	p. 215
Threading and Fold Recognition	p. 223
Ab Initio Protein Structural Prediction	p. 227
CASP	p. 228
Summary	p. 229
Further Reading	p. 230
RNA Structure Prediction	p. 231
Introduction	p. 231
Types of RNA Structures	p. 233
RNA Secondary Structure Prediction Methods	p. 234
Ab Initio Approach	p. 234
Comparative Approach	p. 237
Performance Evaluation	p. 239
Summary	p. 239
Further Reading	p. 240
Genomics and Proteomics
Genome Mapping, Assembly, and Comparison	p. 243
Genome Mapping	p. 243
Genome Sequencing	p. 245
Genome Sequence Assembly	p. 246
Genome Annotation	p. 250
Comparative Genomics	p. 255
Summary	p. 259
Further Reading	p. 259
Functional Genomics	p. 261
Sequence-Based Approaches	p. 261
Microarray-Based Approaches	p. 267
Comparison of SAGE and DNA Microarrays	p. 278
Summary	p. 279
Further Reading	p. 280
Proteomics	p. 281
Technology of Protein Expression Analysis	p. 281
Posttranslational Modification	p. 287
Protein Sorting	p. 289
Protein-Protein Interactions	p. 291
Summary	p. 296
Further Reading	p. 296
Appendix
Practical Exercises	p. 301
Glossary	p. 318
Index	p. 331
Table of Contents provided by Ingram. All Rights Reserved.

Essential Bioinformatics

At a Glance

Paperback

Industry Reviews

Shipping

How to return your order

Defective items

You Can Find This Book In

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