Bioinformatics Bacics

by Rashidi, Hooman H.; Buehler, Lukas K.

• ISBN13: 9780849323751
• ISBN10: 0849323754
• Format: Hardcover
• Copyright: 1999-12-01
• Publisher: CRC Pr I Llc

Summary

Scientists in the throes of research use an extensive data bank to access structural information on proteins and nucleic acids. Meanwhile, geneticists use a highly specialized form of software to analyze the hybridization pattern of DNA chips. The past decade has been tremendously successful for biotechnology and pharmaceutical industries. This success has been a result of astounding technical advancements in genome sequencing (genomics), protein identification (proteomics), and data analysis-collectively called bioinformatics. The exponential increase in computer processing and disk storage has served as a catalyst and been instrumental in the development of bioinformatics. Bioinformatics Basics: Applications in Biological Science and Medicine describes the origin of this field and the organization of public domain databases with an introductory tutorial for the services described. This book explains these services in a relatively simple fashion. Nevertheless, a biological background is necessary to understand and properly utilize the various software components and services described in this book. A basic biological background is also necessary for understanding the biological and medical significance of the collected data. Bioinformatics Basics is a fast growing field, and it will take some years for a stabilization to occur. Until then, hundreds of Internet sites allow us to search, compare, and manipulate this data in its relatively raw format. Bioinformatics Basics: Applications in Biological Science and Medicine concentrates on three major database clusters and relevant software tools that are maintained in the United States, Europe, and Japan, offering free access and analysis through the Internet.

Author Biography

Hooman Rashidi, M.S. has been a biological science instructor, researcher, and bioinformatics consultant. He is the founder of The STD Prevention Program in San Diego. Hooman is a graduate of the University of California at San Diego, where he received a degree with highest honors and departmental distinction in biochemistry and cellular biology. Lukas K. Buehler, Ph.D. has a degree in biochemistry from the University of Basel, Switzerland. He is the founder of whatislife.com, an Internet forum for the advancement of scientific literacy and is a lecturer in the biology department at the University of California at San Diego.

Table of Contents

Preface
Introduction to Bioinformatics	1	(32)
Biology and Bioinformatics	1	(8)
The Nature of Publicly Funded Research	3	(3)
Genomics and Proteomics	6	(1)
Metabolic Databases	6	(1)
Public and Proprietary Bioinformatics	7	(2)
Computers in Biology and Medicine	9	(8)
Computer Algorithms	10	(1)
Different Types of Computers for Different Tasks	11	(1)
Supercomputers	12	(1)
Limitations of Computational Tools: Paradoxical Promise of the Internet	13	(2)
The Need for Computational Tools	15	(1)
New Approaches to Scientific Research with Computers	16	(1)
Biological Macromolecules	17	(16)
Proteins	17	(3)
Protein Structure	20	(2)
Protein Folding	22	(3)
Protein Functions	25	(2)
DNA and RNA Structure	27	(1)
Nucleic Acid Structure and Function	27	(2)
Genetic Code	29	(2)
Genes and Evolution	31	(2)
Databases and Search Tools	33	(50)
Computational Tools and Databases	33	(33)
National Center for Biotechnology Information (NCBI)	34	(10)
European Bioinformatics Institute (EBI)	44	(10)
GenomeNet --- Japanese Bioinformatics Servers	54	(12)
Database Mining Tools	66	(17)
Sequence Similarity Search Tools: BLAST	66	(14)
Pattern Recognition Tools and Databases	80	(3)
Genome Analysis	83	(46)
DNA Cloning and PCR	83	(7)
DNA Cloning	84	(1)
Transcriptional Profiling	85	(1)
Positional Cloning	86	(1)
Polymerase Chain Reaction: PCR	87	(1)
Sequencing Technologies Under Development	88	(1)
Monitoring Sequencing Progress	89	(1)
Computational Tools for DNA Sequence Analysis	90	(17)
Database Submissions	91	(5)
Data Retrieval	96	(3)
Sequence Alignment	99	(2)
What a Sequence Reveals About the Biological Function of a Gene	101	(1)
How to Identify a Gene: ORFs and URFs	102	(2)
A Word About Redundancy	104	(1)
Better Search Engines for Better Computers?	104	(3)
Genome Analysis	107	(13)
Genome Organization	107	(5)
Mapping the Genome	112	(6)
Human Genome Mapping Progress	118	(2)
Functional Genomics	120	(9)
Unidentified Reading Frames: URFs	123	(1)
Cluster of Orthologous Groups: COGs	124	(5)
Proteome Analysis	129	(14)
Proteomics	129	(8)
2-D Page at Expasy	134	(2)
Yeast Proteome Database	136	(1)
Metabolic Reconstruction	137	(6)
KEGG: Kyoto Encyclopedia of Genes and Genomes	137	(1)
The Functional Reconstruction Model	138	(1)
E. coli Metabolic Database: EcoCyc	139	(1)
Where Should We Be in the Future?	140	(3)
The Computer Revolution in Neurobiology	143	(26)
Human Brain Project	143	(11)
The Influence of Computers in Science	144	(1)
Computers in Neurobiology and the Mapping of the Human Brain	145	(4)
From Molecules to Neurodegenerative Diseases	149	(5)
Computer Simulations and Visualization of Molecular Structures	154	(5)
3-D Visualization	154	(3)
The Virtual Doctor: (Virtual and Remote Surgery)	157	(2)
Predictive Biology	159	(10)
Protein Structure Prediction	160	(6)
Structure Prediction Software	166	(3)
Glossary	169	(4)
Index	173