Bioinformatics Basics

Name: Bioinformatics Basics
Brand: Taylor & Francis Inc
Price: 314.25 AUD
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Applications in Biological Science and Medicine

By: Hooman H. Rashidi (Editor), Lukas K. Buehler (Editor)

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Hardcover | 23 June 2005 | Edition Number 2

At a Glance

Hardcover
368 Pages

Edition Type
New edition

Dimensions(cm)
23.4 x 15.6 x 3.18

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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 communityâs need to learn about the bioinformatic tools available to them. That the book continues to be a best seller clearly demonstrates the authorsâ 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, itâs designed to help the general scientific community gain a thorough understanding of what bioinformatics tools are ava

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Non-Fiction Engineering & Technology Biochemical Engineering Biotechnology Science Biology, Life Sciences Computing & I.T.Computer Science Medicine Medicine in General

Biology and Information	p. 1
Bioinformatics-A Rapidly Maturing Science	p. 1
From Genes to Proteins	p. 2
Bioinformatics in the Public Domain	p. 7
Computers in Biology and Medicine	p. 12
Computational Tools	p. 12
Limitations of Computational Tools	p. 18
References	p. 23
The Virtual Doctor	p. 23
Mapping the Human Brain	p. 25
References	p. 30
Biological Macromolecules as Information Carriers	p. 30
References	p. 34
Proteins: From Sequence to Structure to Function	p. 34
Molecular Interaction in Protein Structures	p. 35
The Peptide Bond	p. 35
Characteristics of the Peptide Bond	p. 37
The Hydrophobic Effect and How It Contributes to Protein Folding	p. 39
Electrostatic Interactions	p. 41
Hydrogen Bonding	p. 41
Conformational Entropy	p. 42
Van der Waals Interactions (Packing)	p. 42
Covalent Bonds (e.g., Disulfide Bridge)	p. 42
Protein Functions	p. 42
Enzymes	p. 42
Regulatory Proteins	p. 43
Storage	p. 43
Transportation	p. 43
Signaling	p. 43
Immunity	p. 44
Structural	p. 44
References	p. 44
DNA and RNA Structure	p. 45
The DNA Double Helix	p. 46
Genomic Size of DNA	p. 48
References	p. 49
DNA Cloning and Sequencing	p. 49
DNA Cloning	p. 50
Transcriptional Profiling	p. 51
Positional Cloning and Chromosome Mapping	p. 52
Polymerase Chain Reaction (PCR)	p. 54
Sequencing Technologies	p. 55
References	p. 56
Genes, Taxonomy, and Evolution	p. 56
References	p. 61
Biological Databases	p. 63
Biological Database Organization	p. 63
Database Content and Management	p. 63
Data Submissions	p. 64
The Growth of Public Databases	p. 68
Data Retrieval	p. 70
References	p. 74
Data Annotation and Database Connectivity	p. 75
Annotation	p. 76
Redundancy	p. 78
Public Databases	p. 79
National Center for Biotechnology Information (NCBI)	p. 79
Who is Employed by NCBI?	p. 81
What Kind of Research is Conducted at NCBI?	p. 81
What Types of Databases are Supported by NCBI?	p. 81
What Do We Mean by Redundancy?	p. 82
What are Some of the Services Offered by NCBI?	p. 84
References	p. 89
European Bioinformatics Institute (EBI)	p. 90
Who is Employed by EBI?	p. 90
What Kind of Research is Conducted at EBI?	p. 90
What Are Some Of The Services Offered By EBI?	p. 92
References	p. 101
Kyoto Encyclopedia of Genes and Genomes (KEGG)	p. 102
Classification of Biological Molecules	p. 112
Cellular Processes at KEGG	p. 114
References	p. 117
Database Mining Tools	p. 118
Sequence Similarity Search Tools: BLAST and FASTA	p. 118
Shared Characteristics in Both Sequence Alignment Tools	p. 120
How are Sequence Alignments Useful?	p. 121
Basic Local Alignment Search Tool (BLAST)	p. 122
An Overview of Database Sequence Searching	p. 129
References	p. 131
Pattern Recognition Tools (Prosite)	p. 132
The Significance of Embedded Symbols within Each Signature and How to Read and Construct Signatures	p. 133
References	p. 134
Multiple Alignment and Phylogenetic Tree Analysis	p. 134
References	p. 137
Genome Analysis	p. 139
The Genomic Organization of Genes	p. 139
What are Genomes?	p. 139
Mapping and Navigating Genomes	p. 142
Genetic Linkage Maps	p. 147
Physical Maps	p. 149
From Sequence Maps to Gene Function Maps	p. 154
References	p. 154
The Genome Projects	p. 155
How Many Genes are in a Genome?	p. 158
References	p. 164
The Human Genome	p. 164
References	p. 169
Comparative Genomics	p. 170
Cluster of Orthologous Groups (COGs)	p. 170
Homologene at NCBI	p. 176
References	p. 182
Gene Order and Chromosome Rearrangements	p. 182
MapViewer	p. 183
References	p. 185
Functional Genomics	p. 185
The Transcriptome	p. 185
Microarray and Bioarray Technology	p. 190
Concept and Use	p. 190
Summary of a Typical Experiment Using Microarray Technology	p. 191
Microarray Bioinformatics	p. 191
Image Processing	p. 194
References	p. 195
Data Annotation	p. 195
References	p. 196
Data Analysis	p. 196
Experiment Design/Plan	p. 197
Volume of Data	p. 197
Dimensionality of Data	p. 199
Quality of Data	p. 199
Normalization	p. 199
Statistical Analysis	p. 199
Explorative Analysis	p. 202
Aim of Clustering	p. 202
Biological Interpretation of Clustering Results	p. 202
Theory of Clustering	p. 202
Clustering vs. Classification (Unsupervised vs. Supervised)	p. 203
Main Types of Clustering	p. 203
Hierarchical Clustering	p. 203
Nonhierarchical Clustering	p. 204
Other Clustering or Classification Algorithms	p. 206
Advice on Using Clustering	p. 206
References	p. 207
Data Storage	p. 208
References	p. 209
Data Mining	p. 209
Protein Arrays	p. 209
Concluding Remarks	p. 211
Genomes as Gene Networks	p. 211
References	p. 216
Proteome Analysis	p. 217
Proteomics	p. 217
What is a Proteome?	p. 217
2-D Gels and Mass Spectrometry Tools	p. 219
2-D PAGE at Expasy (Swiss Bioinformatics Institute)	p. 221
References	p. 225
Hydrodynamic Methods	p. 226
Introduction	p. 226
Analytical Ultracentrifugation	p. 228
Experimental Setup and Instrumentation	p. 228
Transport Processes in The AUC Cell	p. 229
Analytical Ultracentrifuge (AUC) Experiments	p. 234
Light Scattering	p. 246
Experimental Setup and Instrumentation	p. 246
Dynamic Light Scattering	p. 247
Static Light Scattering	p. 250
Global Analysis	p. 252
Appendix	p. 254
References	p. 255
Predictive Biology	p. 256
Protein Structure Prediction	p. 256
Structure Prediction Software	p. 266
References	p. 269
Structural Genomics	p. 269
References	p. 276
Rational Drug Design	p. 276
References	p. 285
Systems Biology	p. 285
Protein Interaction Networks	p. 285
References	p. 290
Metabolic Reconstruction	p. 290
References	p. 295
The Bioinformatics Revolution in Medicine	p. 297
Genes and Diseases	p. 297
From Molecules to Diseases	p. 297
References	p. 303
Online Mendelian Inheritance in Man (OMIM)	p. 303
References	p. 308
Pharmacogenomics	p. 308
Agricultural Genomics	p. 309
Genetically Modified Organisms	p. 312
References	p. 313
Biopharming	p. 313
References	p. 316
Glossary of Biological Terms	p. 317
Bioinformatics Web Sites	p. 323
Index	p. 325
Table of Contents provided by Ingram. All Rights Reserved.

Bioinformatics Basics

Applications in Biological Science and Medicine

At a Glance

Hardcover

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