This clear and concise introduction to bioinformatics will appeal to undergraduate and graduate students in the life sciences, as well as researchers wishing to develop their knowledge of bioinformatics tools. All key areas are covered including biological databases, sequence alignment, genes and promoter prediction, molecular phylogenetics, structural bioinformatics, genomics and proteomics. (www.amazon.de)Pressestimmen'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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Preface 11II ix
SECTION I INTRODUCTION AND BIOLOGlCAL DATABASES
I Introductlon 11I 3
What Is Bioinformaties? 11 4
Goal 11I 5
Scope 11II 5
Applications 11 6
Limitations 11II 7
New Themes 11II 8
Purther Reading 11II 8
2 Introduction to Biological Databases 11II 10
What Is a Database? 11I 10
Types ofDatabases 11 10
Biological Databases 11II 13
Pitfalls of Biological Databases 11II 17
Information Retrieval from Biological Databases 11I 18
Summary 11I 27
Purther Reading 11II 27
SECTION II SEQUENCE ALIGNMENT
3 Pairwise Sequence Alignment 11II 31
Evolutionary Basis 11II 31
Sequence Homology versus Sequence Similarity 11I 32
Sequence Similarity versus Sequence Identity 11I 33
Methods 11II 34
Scoring Matrices 11II 41
Statistical Significance of Sequence AIignment 11I 47
Summary 11II 48
Further Reading 11 49
4 Database Similarity Searchlng 11II 51
Unique Requirements of Database Searehing 11II 51
Heuristic Database Searching 11II 52
Basic Loeal AIignment Seareh Tool (BLAST) 11 52
PASTA 11I 57
Comparison of PASTA and BLAST 11I 60
Database Searching with the Smith-Waterman Method 11II 61
Summary l1li 61
further Reading l1li 62
5 Multiple Sequence Alignment l1li 63
Scoring Function 111 63
Exhaustive Algorithms I11III 64
Heuristic Algorithms 111 65
PracticalIssues 11 71
Summary 11 73
further Reading 11 74
6 Profiles and Hidden Markov Models 111 75
Position-Specific Scoring Matrices 11 75
Profiles lIIi 77
Markov Model and Hidden Markov Model. 79
Summary 111 84
further Reading 111 84
7 Protein Motifs and Domain Prediction .i 85
Identification of'Motifs and Domains in Multiple Sequence
Alignment 111 86
Motif and Domain Databases Using Regular Expressions 111 86
Motif and Domain Databases Using Statistical Models 111 87
Pro tein Family Databases o 90
Motif Discovery in Unaligned Sequences 111 91
Sequence Logos o 92
Summary lIIi 93
further Reading .i 94
SECTION III GENE AND PROMOTER PREDICTION
8 Gene Prediction I11III 97
Categories of Gene Prediction Programs I11III; 97
Gene Prediction in Prokaryotes 111 98
Gene Prediction in Eukaryotes 111 103
Summary 111 111
Further Reading 111 111
9 Promoter and Regulatory Element Prediction 111 113
Promoter and Regulatory Elements in Prokaryotes .i 113
Promoter and Regulatory Elements in Eukaryotes 111 114
Prediction Aigorithms 111 115
Summary 111 123
Further Reading 111 124
SECTION IV MOLECULAR PHYLOGENETICS
10 Phylogenetics Basics I11III 127
Molecular Evolution and Molecular Phylogenetics 111 127
Terminology o 128
Gene Phylogeny versus Species Phylogeny o 130
Forms ofTree Representation II!I 131
Why Finding a True Tree Is Difficult 111 132
Procedure 111 133
Summary 111 140
Further Reading 111 141
11 Phylogenetic Tree Construction Methods and Programs 111 142
Distance- Based Methods 111 142
Character- Based Methods 111 150
Phylogenetic Tree Evaluation 111 163
Phylogenetic Programs 111 167
Summary 111 168
Further Reading II!I 169
SECTION V STRUCTURAL BIOINFORMATICS
12 Protein Structure Basics 111 173
Amino Acids 111 173
Peptide Formation 111 174
Dihedral Anglesa 175
Hierarchy 111 176
Secondary Structures 111 178
Tertiary Structures 111 180
Determination of Pro tein Three- Dimensional Structure 111 181
Protein Structure Database 111 182
Summary 111 185
Further Reading 111 186
13 Protein Structure Visualization, Comparison,
and Classification 111 187
Pro tein Structural Visualization 111 187
Pro tein Structure Comparison 111 190
Pro tein Structure Classification 111 195
Summary 111 199
Further Reading 111 199
14 Protein Secondary Structure Predietion II!I 200
Secondary Structure Prediction for Globular Proteins 111 201
Secondary Structure Prediction for Transmembrane Proteins 111 208
Coiled CoiI Prediction 111 211
Summary 111 212
Further Reading 111 213
15 Protein Tertiary Structure Prediction o 214
Methods 111 215
HomologyModeling 111 215
Threading and Fold Recognition 111 223
Ab Initio Protein Structural Prediction 111 227
CASP 111 228
Summary 111 229
Further Reading o 230
16 RNA Structure Prediction l1li 231
Introduction 11 231
Types of RNA Structures llII 233
RNA Secondary Structure Prediction Methods lllJ 234
Ab Initio Approach liIII 234
Comparative Approach m 237
Performance Evaluation 11 239
Summary lIl! 239
further Reading m 240
SECTION VI GENOMICS AND PROTEOMICS
17 Genome Mapping, Assembly; and Comparison m 243
Genome Mapping lIIl 243
Genome Sequencing llII 245
Genome Sequence Assembly lI!l 246
Genome Annotation lIIl 250
Comparative Genomics lIl! 255
Summary lIl! 259
Further Reading lIIiI 259
18 Functional Genomics 11 261
Sequence-Based Approaches lIIl 261
Microarray-Based Approaches l1li 267
Comparison ofSAGE and DNA Microarrays l1li 278
Summary 11 279
Further Reading lI!iI Z8G
19 Proteomics lI!iI 281
Technology ofProtein Expression Analysis lI!iI 281
Posttranslational Modification l1li 287
Protein Sorting 11 289
Protein-Protein Interactions lIIiI 291
Summary lI!iI 296
Further Reading lI!iI 296
APPENDIX
Appendix I. Practical Exercises 11 301
Appendix 2. Glossary lI!iI 318
Index 111 331