Introduction to Bioinformatics

by Karwetz, Stephen A., Ph.D.; Womble, David D., Ph.D.

• ISBN13: 9781588292414
• ISBN10: 158829241X
• Edition: CD
• Format: Paperback
• Copyright: 2003-02-01
• Publisher: Humana Pr Inc

Summary

Introduction to Bioinformatics: A Theoretical and Practical Approach was written as an introductory text for the undergraduate, graduate, or professional. This text provides scientists with both a biological framework to understand the questions life scientist confront in the context of the computational issues and tools that are currently available for scientific research It also provides the life scientist with a resource to the various computational tools that are available all supported with their underlying mathematical foundations. The book is divided into four main sections. The first two sections provide an overview of the various biological processes that govern an organism and impact health. The first section, Biochemistry, Cell and Molecular Biology, describes basic cellular structure and the decoding of the genome. The second section, Molecular Genetics covers the regulation of genomes and the molecular genetic basis of disease as a consequence of genetic replication. Clinical human genetics and the various clinical databases are also reviewed. The third section, the Unix Operating System, demystifies the Unix system used throughout the world to support advanced computation tools. In addition to information on the installation and management of Unix-based software tools, examples of command line sequence analyses are presented that will enable the research to become as comfortable in a command-line environment as they are in the Graphical-User Interface environment. The final section, Computer Applications, provides information on the management and analysis of DNA sequencing projects, along with a review of how DNA can be modeled as a statistical series of patterns. It follows with a discussion of the various genome databases, the representation of genomes, and methods for their large scale analyses. Protein visualization, and transcription profiling including the use of analysis software for systems biology round out the coverage. The volume also includes a bonus CD-ROM containing valuable software programs including BioDiscovery (for microarray analysis), ClustalX (a sequence alignment program) Ensembl, MicroAnalyser (for microarray analysis on the Macintosh), Staden Sequence Analysis Package, Tree View (for displaying phylogenies) an others. Also included is a complete set of color illustrations from each chapter that will prove invaluable for professors preparing their next bioinformatics course or seminar.

Table of Contents

Preface	v
Contributors	xi
Part I. Biochemistry, Cell, and Molecular Biology:
A. The Cell
Nucleic Acids and Proteins: Modern Linguistics for the Genomics and Bioinformatics Era	5	(20)
Bradley C. Hyman
Structure and Function of Cell Organelles	25	(30)
Jon Holy
Cell Signaling	55	(20)
Daniel A. Rappolee
B. Transcription and Translation
DNA Replication, Repair, and Recombination	75	(18)
Linda B. Bloom
Transcription, RNA Processing, and Translation	93	(30)
Thomas P. Yang
Thomas W. O'Brien
Part II. Molecular Genetics:
A. Genomics
Epigenetic Mechanisms Regulating Gene Expression	123	(18)
John R. McCarrey
Gene Families and Evolution	141	(10)
Ben F. Koop
Repetitive DNA: Detection, Annotation, and Analysis	151	(18)
Jerzy Jurka
Molecular Genetics of Disease and the Human Genome Project	169	(18)
Paromita Deb-Rinker
Stephen W. Scherer
B. Clinical Human Genetics
Heredity	187	(12)
C. A. Rupar
The Clinical Genetics Databases	199	(8)
Peter J. Bridge
Population Genetics	207	(26)
Jill S. Barnholtz-Sloan
Part III. The UNIX Operating System:
A. Basics and Installation
Introduction to UNIX for Biologists	233	(14)
David D. Womble
Installation of the Sun Solaris™ Operating Environment	247	(16)
Bryon Campbell
Sun System Administration	263	(22)
Bryon Campbell
B. Managing Bioinformatics Tools
Installing Bioinformatics Software in a Server-Based Computing Environment	285	(12)
Brian Fristensky
Management of a Server-Based Bioinformatics Resource	297	(12)
Brian Fristensky
C. Command Line Sequence Analysis
GCG File Management	309	(6)
Sittichoke Saisanit
GCG Sequence Analysis	315	(12)
Sittichoke Saisanit
Part IV. Computer Applications:
A. Management and Analysis of DNA Sequencing Projects and Sequences
Managing Sequencing Projects in the GAP4 Environment	327	(18)
Rodger Staden
David P. Judge
James K. Bonfield
OLIGO Primer Analysis Software	345	(12)
John D. Offerman
Wojciech Rychlik
Statistical Modeling of DNA Sequences and Patterns	357	(18)
Gautam B. Singh
Statistical Mining of the Matrix Attachment Regions in Genomic Sequences	375	(18)
Gautam B. Singh
Analyzing Sequences Using the Staden Package and EMBOSS	393	(20)
Rodger Staden
David P. Judge
James K. Bonfield
B. The Genome Database: Analysis and Similarity Searching
Ensembl: An Open-Source Software Tool for Large-Scale Genome Analysis	413	(18)
James W. Stalker
Anthony V. Cox
The PIR for Functional Genomics and Proteomics	431	(12)
Cathy H. Wu
Sequence Similarity and Database Searching	443	(20)
David S. Wishart
GCG Database Searching	463	(28)
David J. Heard
C. Identifying Functional and Structural Sequence Elements
Pattern Discovery: Methods and Software	491	(32)
Brona Brejova
Tomas Vinar
Ming Li
The Role of Transcription Factor Binding Sites in Promoters and Their In Silico Detection	523	(16)
Thomas Werner
An Introduction to Multiple Sequence Alignment and Analysis	539	(26)
Steven M. Thompson
3D Molecular Visualization with Protein Explorer	565	(22)
Eric Martz
Multiple Sequence Alignment and Analysis: The SeqLab Interface: A Practical Guide	587	(50)
Steven M. Thompson
D. Analysis of Gene Expression: Microarrays and Other Tools
Overview of the Tools for Microarray Analysis: Transcription Profiling, DNA Chips, and Differential Display	637	(28)
Jeffrey A. Kramer
Microarrays: Tools for Gene Expression Analysis	665	(28)
Sorin Draghici
Knowledge Discovery from the Human Transcriptome	693	(32)
Kousaku Okubo
Teruyoshi Hishiki
Part V. Appendices:
Appendix 1: CD Contents	715	(4)
Appendix 2: A Collection of Useful Bioinformatic Tools and Molecular Tables	719	(4)
Appendix 3: Simple UNIX Commands	723	(2)
Index	725