Bioinformatics basics : applications in biological science and medicine

Library	Item Barcode	Call Number	Material Type	Item Category 1	Status
Searching... PSZ JB	30000004720672	QH324.2 B568 2005	Open Access Book	Book	Searching... Unknown
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Every researcher in genomics and proteomics now has access to public domain databases containing literally billions of data entries. However, without the right analytical tools, and an understanding of the biological significance of the data, cataloging and interpreting the molecular evolutionary processes buried in those databases is difficult, if not impossible.

The first editon of Bioinformatics Basics: Applications in Biological Science and Medicine answered the scientific community's need to learn about the bioinformatic tools available to them. That the book continues to be a best seller clearly demonstrates the authors' ability to provide scientists with the understanding to apply those tools to their research. Currently, it is being used as a reference text at MIT and other prestigious institutions.

Recognizing the important advances in bioinformatices since their last edition, Buehler and Rashidi have produced a completely revised and updated version of their pioneering work. To allow scientists to utilize significant databases from around the world, the authors consider some fresh approaches to data analysis while identifying computing techniques that will help them manage the massive flow of information their science requires.

New to the second edition:

Provides a more detailed view of the field while continuing to focus on the global concept approach that popularized the first edition. Offers the latest approaches to data analysis Introduces recent developments in genomics, microarrays, proteomics, genome mapping, and more. Adds two new sections offering insights from other experts in bioinformatics.

Bioinformatics Basics is not intended to serve as a training manual for bioinformaticians. Instead, it's designed to help the general scientific community gain a thorough understanding of what bioinformatics tools are ava

Author Notes

Lukas K. Buehler, Hooman H. Rashidi

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Within the past decade advances in computers, optics, the Internet, and molecular biology have led to the accumulation of vast amounts of data about the nature of DNA, RNA, and proteins. Bioinformatics encompasses the large suite of computational tools that are used to analyze this data, turning it into useful information. This completely revised and expanded edition is divided into five chapters, the first of which serves to introduce the nonbiologist to the biological information-carrying molecules and the methods used by labs to generate sequence data from organisms. The second chapter describes and summarizes key resources available from the three major data depositories--the National Center for Biotechnology Information, the European Bioinformatics Institute, and Japan's GenomeWeb . The remaining chapters give an overview of the bioinformatics tools that are used to analyze genomic and protein data, with examples primarily from medicine. This is not a methods or training manual; rather, it will give novice biologists and computer scientists a brief look at the commonly employed bioinformatics resources and the types of questions they can answer. The book is well indexed and has informative tables and figures (some in color). ^BSumming Up: Recommended. Upper-level undergraduates and graduate students. K. A. Newman University of Illinois at Urbana-Champaign

1 Biology and Information	p. 1
1.1 Bioinformatics-A Rapidly Maturing Science	p. 1
1.1.1 From Genes to Proteins	p. 2
1.1.2 Bioinformatics in the Public Domain	p. 7
1.2 Computers in Biology and Medicine	p. 12
1.2.1 Computational Tools	p. 12
1.2.2 Limitations of Computational Tools	p. 18
References	p. 23
1.3 The Virtual Doctor	p. 23
1.3.1 Mapping the Human Brain	p. 25
References	p. 30
1.4 Biological Macromolecules as Information Carriers	p. 30
References	p. 34
1.5 Proteins: From Sequence to Structure to Function	p. 34
1.5.1 Molecular Interaction in Protein Structures	p. 35
1.5.1.1 The Peptide Bond	p. 35
1.5.1.2 Characteristics of the Peptide Bond	p. 37
1.5.1.3 The Hydrophobic Effect and How It Contributes to Protein Folding	p. 39
1.5.1.4 Electrostatic Interactions	p. 41
1.5.1.5 Hydrogen Bonding	p. 41
1.5.1.6 Conformational Entropy	p. 42
1.5.1.7 Van der Waals Interactions (Packing)	p. 42
1.5.1.8 Covalent Bonds (e.g., Disulfide Bridge)	p. 42
1.5.2 Protein Functions	p. 42
1.5.2.1 Enzymes	p. 42
1.5.2.2 Regulatory Proteins	p. 43
1.5.2.3 Storage	p. 43
1.5.2.4 Transportation	p. 43
1.5.2.5 Signaling	p. 43
1.5.2.6 Immunity	p. 44
1.5.2.7 Structural	p. 44
References	p. 44
1.6 DNA and RNA Structure	p. 45
1.6.1 The DNA Double Helix	p. 46
1.6.2 Genomic Size of DNA	p. 48
References	p. 49
1.7 DNA Cloning and Sequencing	p. 49
1.7.1 DNA Cloning	p. 50
1.7.2 Transcriptional Profiling	p. 51
1.7.3 Positional Cloning and Chromosome Mapping	p. 52
1.7.4 Polymerase Chain Reaction (PCR)	p. 54
1.7.5 Sequencing Technologies	p. 55
References	p. 56
1.8 Genes, Taxonomy, and Evolution	p. 56
References	p. 61
2 Biological Databases	p. 63
2.1 Biological Database Organization	p. 63
2.1.1 Database Content and Management	p. 63
2.1.2 Data Submissions	p. 64
2.1.3 The Growth of Public Databases	p. 68
2.1.4 Data Retrieval	p. 70
References	p. 74
2.1.5 Data Annotation and Database Connectivity	p. 75
2.1.5.1 Annotation	p. 76
2.1.5.2 Redundancy	p. 78
2.2 Public Databases	p. 79
2.2.1 National Center for Biotechnology Information (NCBI)	p. 79
2.2.1.1 Who is Employed by NCBI?	p. 81
2.2.1.2 What Kind of Research is Conducted at NCBI?	p. 81
2.2.1.3 What Types of Databases are Supported by NCBI?	p. 81
2.2.1.4 What Do We Mean by Redundancy?	p. 82
2.2.1.5 What are Some of the Services Offered by NCBI?	p. 84
References	p. 89
2.2.2 European Bioinformatics Institute (EBI)	p. 90
2.2.2.1 Who is Employed by EBI?	p. 90
2.2.2.2 What Kind of Research is Conducted at EBI?	p. 90
2.2.2.3 What Are Some Of The Services Offered By EBI?	p. 92
References	p. 101
2.2.3 Kyoto Encyclopedia of Genes and Genomes (KEGG)	p. 102
2.2.3.1 Classification of Biological Molecules	p. 112
2.2.3.2 Cellular Processes at KEGG	p. 114
References	p. 117
2.3 Database Mining Tools	p. 118
2.3.1 Sequence Similarity Search Tools: BLAST and FASTA	p. 118
2.3.1.1 Shared Characteristics in Both Sequence Alignment Tools	p. 120
2.3.1.2 How are Sequence Alignments Useful?	p. 121
2.3.1.3 Basic Local Alignment Search Tool (BLAST)	p. 122
2.3.2 An Overview of Database Sequence Searching	p. 129
References	p. 131
2.3.3 Pattern Recognition Tools (Prosite)	p. 132
2.3.3.1 The Significance of Embedded Symbols within Each Signature and How to Read and Construct Signatures	p. 133
References	p. 134
2.3.4 Multiple Alignment and Phylogenetic Tree Analysis	p. 134
References	p. 137
3 Genome Analysis	p. 139
3.1 The Genomic Organization of Genes	p. 139
3.1.1 What are Genomes?	p. 139
3.1.2 Mapping and Navigating Genomes	p. 142
3.1.2.1 Genetic Linkage Maps	p. 147
3.1.2.2 Physical Maps	p. 149
3.1.2.3 From Sequence Maps to Gene Function Maps	p. 154
References	p. 154
3.1.2 The Genome Projects	p. 155
3.1.2.1 How Many Genes are in a Genome?	p. 158
References	p. 164
3.1.3 The Human Genome	p. 164
References	p. 169
3.2 Comparative Genomics	p. 170
3.2.1 Cluster of Orthologous Groups (COGs)	p. 170
3.2.2 Homologene at NCBI	p. 176
References	p. 182
3.2.2.1 Gene Order and Chromosome Rearrangements	p. 182
3.2.2.2 MapViewer	p. 183
References	p. 185
3.3 Functional Genomics	p. 185
3.3.1 The Transcriptome	p. 185
3.4 Microarray and Bioarray Technology	p. 190
3.4.1 Concept and Use	p. 190
3.4.2 Summary of a Typical Experiment Using Microarray Technology	p. 191
3.4.3 Microarray Bioinformatics	p. 191
3.4.4 Image Processing	p. 194
References	p. 195
3.4.5 Data Annotation	p. 195
References	p. 196
3.4.6 Data Analysis	p. 196
3.4.6.1 Experiment Design/Plan	p. 197
3.4.6.2 Volume of Data	p. 197
3.4.6.3 Dimensionality of Data	p. 199
3.4.6.4 Quality of Data	p. 199
3.4.7 Normalization	p. 199
3.4.8 Statistical Analysis	p. 199
3.4.9 Explorative Analysis	p. 202
3.4.9.1 Aim of Clustering	p. 202
3.4.9.2 Biological Interpretation of Clustering Results	p. 202
3.4.9.3 Theory of Clustering	p. 202
3.4.9.4 Clustering vs. Classification (Unsupervised vs. Supervised)	p. 203
3.4.10 Main Types of Clustering	p. 203
3.4.10.1 Hierarchical Clustering	p. 203
3.4.10.2 Nonhierarchical Clustering	p. 204
3.4.10.3 Other Clustering or Classification Algorithms	p. 206
3.4.10.4 Advice on Using Clustering	p. 206
References	p. 207
3.4.11 Data Storage	p. 208
References	p. 209
3.4.12 Data Mining	p. 209
3.4.13 Protein Arrays	p. 209
3.4.14 Concluding Remarks	p. 211
3.5 Genomes as Gene Networks	p. 211
References	p. 216
4 Proteome Analysis	p. 217
4.1 Proteomics	p. 217
4.1.1 What is a Proteome?	p. 217
4.1.1.1 2-D Gels and Mass Spectrometry Tools	p. 219
4.1.1.2 2-D PAGE at Expasy (Swiss Bioinformatics Institute)	p. 221
References	p. 225
4.2 Hydrodynamic Methods	p. 226
4.2.1 Introduction	p. 226
4.2.2 Analytical Ultracentrifugation	p. 228
4.2.2.1 Experimental Setup and Instrumentation	p. 228
4.2.2.2 Transport Processes in The AUC Cell	p. 229
4.2.2.3 Analytical Ultracentrifuge (AUC) Experiments	p. 234
4.2.3 Light Scattering	p. 246
4.2.3.1 Experimental Setup and Instrumentation	p. 246
4.2.3.2 Dynamic Light Scattering	p. 247
4.2.3.3 Static Light Scattering	p. 250
4.2.4 Global Analysis	p. 252
4.2.5 Appendix	p. 254
References	p. 255
4.3 Predictive Biology	p. 256
4.3.1 Protein Structure Prediction	p. 256
4.3.1.1 Structure Prediction Software	p. 266
References	p. 269
4.3.2 Structural Genomics	p. 269
References	p. 276
4.3.3 Rational Drug Design	p. 276
References	p. 285
4.4 Systems Biology	p. 285
4.4.1 Protein Interaction Networks	p. 285
References	p. 290
4.4.2 Metabolic Reconstruction	p. 290
References	p. 295
5 The Bioinformatics Revolution in Medicine	p. 297
5.1 Genes and Diseases	p. 297
5.1.1 From Molecules to Diseases	p. 297
References	p. 303
5.1.2 Online Mendelian Inheritance in Man (OMIM)	p. 303
References	p. 308
5.1.3 Pharmacogenomics	p. 308
5.2 Agricultural Genomics	p. 309
5.2.1 Genetically Modified Organisms	p. 312
References	p. 313
5.2.2 Biopharming	p. 313
References	p. 316
Appendix A Glossary of Biological Terms	p. 317
Appendix B Bioinformatics Web Sites	p. 323
Index	p. 325

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