Bioinformatics Basics: Applications in Biological Science and Medicine

by Buehler; Lukas K.

• ISBN13: 9780849312830
• ISBN10: 0849312833
• Edition: 2nd
• Format: Hardcover
• Copyright: 2005-06-23
• Publisher: CRC Press

Summary

Completely revised and updated, Bioinformatics Basics: Applications in Biological Science and Medicine, Second Edition will continue to serve as a tool that allows researchers to easily access and use databases to gather information on genes, proteins, and diseases. This new edition of a bestseller covers new approaches to data analysis using databases around the world. It identifies computing techniques that help readers manage the massive flow of information. The structure of this second edition will follow that of the first and its content will reflect the growth in information. New sections cover recent developments in genome projects, microarrays, proteomics, genome mapping, and more.

Table of Contents

1 Biology and Information	1	(62)
1.1 Bioinformatics-A Rapidly Maturing Science	1	(11)
1.1.1 From Genes to Proteins	2	(5)
1.1.2 Bioinformatics in the Public Domain	7	(5)
1.2 Computers in Biology and Medicine	12	(11)
1.2.1 Computational Tools	12	(6)
1.2.2 Limitations of Computational Tools	18	(5)
References	23	(1)
1.3 The Virtual Doctor	23	(7)
1.3.1 Mapping the Human Brain	25	(5)
References	30	(1)
1.4 Biological Macromolecules as Information Carriers	30	(4)
References	34	(1)
1.5 Proteins: From Sequence to Structure to Function	34	(10)
1.5.1 Molecular Interaction in Protein Structures	35	(7)
1.5.1.1 The Peptide Bond	35	(2)
1.5.1.2 Characteristics of the Peptide Bond	37	(2)
1.5.1.3 The Hydrophobic Effect and How It Contributes to Protein Folding	39	(2)
1.5.1.4 Electrostatic Interactions	41	(1)
1.5.1.5 Hydrogen Bonding	41	(1)
1.5.1.6 Conformational Entropy	42	(1)
1.5.1.7 Van der Waals Interactions (Packing)	42	(1)
1.5.1.8 Covalent Bonds (e.g., Disulfide Bridge)	42	(1)
1.5.2 Protein Functions	42	(3)
1.5.2.1 Enzymes	42	(1)
1.5.2.2 Regulatory Proteins	43	(1)
1.5.2.3 Storage	43	(1)
1.5.2.4 Transportation	43	(1)
1.5.2.5 Signaling	43	(1)
1.5.2.6 Immunity	44	(1)
1.5.2.7 Structural	44	(1)
References	44	(1)
1.6 DNA and RNA Structure	45	(4)
1.6.1 The DNA Double Helix	46	(2)
1.6.2 Genomic Size of DNA	48	(1)
References	49	(1)
1.7 DNA Cloning and Sequencing	49	(7)
1.7.1 DNA Cloning	50	(1)
1.7.2 Transcriptional Profiling	51	(1)
1.7.3 Positional Cloning and Chromosome Mapping	52	(2)
1.7.4 Polymerase Chain Reaction (PCR)	54	(1)
1.7.5 Sequencing Technologies	55	(1)
References	56	(1)
1.8 Genes, Taxonomy, and Evolution	56	(5)
References	61	(2)
2 Biological Databases	63	(76)
2.1 Biological Database Organization	63	(11)
2.1.1 Database Content and Management	63	(1)
2.1.2 Data Submissions	64	(4)
2.1.3 The Growth of Public Databases	68	(2)
2.1.4 Data Retrieval	70	(4)
References	74	(5)
2.1.5 Data Annotation and Database Connectivity	75	(4)
2.1.5.1 Annotation	76	(2)
2.1.5.2 Redundancy	78	(1)
2.2 Public Databases	79	(10)
2.2.1 National Center for Biotechnology Information (NCBI)	79	(10)
2.2.1.1 Who is Employed by NCBI?	81	(1)
2.2.1.2 What Kind of Research is Conducted at NCBI?	81	(1)
2.2.1.3 What Types of Databases are Supported by NCBI?	81	(1)
2.2.1.4 What Do We Mean by Redundancy?	82	(2)
2.2.1.5 What are Some of the Services Offered by NCBI?	84	(5)
References	89	(12)
2.2.2 European Bioinformatics Institute (EBI)	90	(11)
2.2.2.1 Who is Employed by EBI?	90	(1)
2.2.2.2 What Kind of Research is Conducted at EBI?	90	(2)
2.2.2.3 What Are Some Of The Services Offered By EBI?	92	(9)
References	101	(16)
2.2.3 Kyoto Encyclopedia of Genes and Genomes (KEGG)	102	(16)
2.2.3.1 Classification of Biological Molecules	112	(2)
2.2.3.2 Cellular Processes at KEGG	114	(3)
References	117	(1)
2.3. Database Mining Tools	118	(13)
2.3.1 Sequence Similarity Search Tools: BLAST and FASTA	118	(11)
2.3.1.1 Shared Characteristics in Both Sequence Alignment Tools	120	(1)
2.3.1.2 How are Sequence Alignments Useful?	121	(1)
2.3.1.3 Basic Local Alignment Search Tool (BLAST)	122	(7)
2.3.2 An Overview of Database Sequence Searching	129	(2)
References	131	(3)
2.3.3 Pattern Recognition Tools (Prosite)	132	(2)
2.3.3.1 The Significance of Embedded Symbols within Each Signature and How to Read and Construct Signatures	133	(1)
References	134	(3)
2.3.4 Multiple Alignment and Phylogenetic Tree Analysis	134	(3)
References	137	(2)
3 Genome Analysis	139	(78)
3.1 The Genomic Organization of Genes	139	(15)
3.1.1 What are Genomes?	139	(3)
3.1.2 Mapping and Navigating Genomes	142	(12)
3.1.2.1 Genetic Linkage Maps	147	(2)
3.1.2.2 Physical Maps	149	(5)
3.1.2.3 From Sequence Maps to Gene Function Maps	154	(1)
References	154	(10)
3.1.2 The Genome Projects	155	(9)
3.1.2.1 How Many Genes are in a Genome?	158	(6)
References	164	(5)
3.1.3 The Human Genome	164	(5)
References	169	(1)
3.2 Comparative Genomics	170	(12)
3.2.1 Cluster of Orthologous Groups (COGs)	170	(6)
3.2.2 Homologene at NCBI	176	(6)
References	182	(3)
3.2.2.1 Gene Order and Chromosome Rearrangements	182	(1)
3.2.2.2 MapViewer	183	(2)
References	185	(1)
3.3 Functional Genomics	185	(5)
3.3.1 The Transcriptome	185	(5)
3.4 Microarray and Bioarray Technology	190	(5)
3.4.1 Concept and Use	190	(1)
3.4.2 Summary of a Typical Experiment Using Microarray Technology	191	(1)
3.4.3 Microarray Bioinformatics	191	(3)
3.4.4 Image Processing	194	(1)
References	195	(1)
3.4.5 Data Annotation	195	(1)
References	196	(11)
3.4.6 Data Analysis	196	(3)
3.4.6.1 Experiment Design/Plan	197	(1)
3.4.6.2 Volume of Data	197	(2)
3.4.6.3 Dimensionality of Data	199	(1)
3.4.6.4 Quality of Data	199	(1)
3.4.7 Normalization	199	(1)
3.4.8 Statistical Analysis	199	(3)
3.4.9 Explorative Analysis	202	(1)
3.4.9.1 Aim of Clustering	202	(1)
3.4.9.2 Biological Interpretation of Clustering Results	202	(1)
3.4.9.3 Theory of Clustering	202	(1)
3.4.9.4 Clustering vs. Classification (Unsupervised vs. Supervised)	203	(1)
3.4.10 Main Types of Clustering	203	(4)
3.4.10.1 Hierarchical Clustering	203	(1)
3.4.10.2 Nonhierarchical Clustering	204	(2)
3.4.10.3 Other Clustering or Classification Algorithms	206	(1)
3.4.10.4 Advice on Using Clustering	206	(1)
References	207	(2)
3.4.11 Data Storage	208	(1)
References	209	(2)
3.4.12 Data Mining	209	(1)
3.4.13 Protein Arrays	209	(2)
3.4.14 Concluding Remarks	211	(1)
3.5 Genomes as Gene Networks	211	(5)
References	216	(1)
4 Proteome Analysis	217	(80)
4.1 Proteomics	217	(8)
4.1.1 What is a Proteome?	217	(9)
4.1.1.1 2-D Gels and Mass Spectrometry Tools	219	(2)
4.1.1.2 2-D PAGE at Expasy (Swiss Bioinformatics Institute)	221	(4)
References	225	(1)
4.2 Hydrodynamic Methods	226	(29)
4.2.1 Introduction	226	(2)
4.2.2 Analytical Ultracentrifugation	228	(18)
4.2.2.1 Experimental Setup and Instrumentation	228	(1)
4.2.2.2 Transport Processes in The AUC Cell	229	(5)
4.2.2.3 Analytical Ultracentrifuge (AUC) Experiments	234	(12)
4.2.3 Light Scattering	246	(6)
4.2.3.1 Experimental Setup and Instrumentation	246	(1)
4.2.3.2 Dynamic Light Scattering	247	(3)
4.2.3.3 Static Light Scattering	250	(2)
4.2.4 Global Analysis	252	(2)
4.2.5 Appendix	254	(1)
References	255	(1)
4.3 Predictive Biology	256	(13)
4.3.1 Protein Structure Prediction	256	(13)
4.3.1.1 Structure Prediction Software	266	(3)
References	269	(7)
4.3.2 Structural Genomics	269	(7)
References	276	(9)
4.3.3 Rational Drug Design	276	(9)
References	285	(1)
4.4 Systems Biology	285	(5)
4.4.1 Protein Interaction Networks	285	(5)
References	290	(5)
4.4.2 Metabolic Reconstruction	290	(5)
References	295	(2)
5 The Bioinformatics Revolution in Medicine	297	(20)
5.1 Genes and Diseases	297	(6)
5.1.1 From Molecules to Diseases	297	(6)
References	303	(5)
5.1.2 Online Mendelian Inheritance in Man (OMIM)	303	(5)
References	308	(1)
5.1.3 Pharmacogenomics	308	(1)
5.2 Agricultural Genomics	309	(4)
5.2.1 Genetically Modified Organisms	312	(1)
References	313	(3)
5.2.2 Biopharming	313	(3)
References	316	(1)
Appendix A Glossary of Biological Terms	317	(6)
Appendix B Bioinformatics Web Sites	323	(2)
Index	325