Introduction to bioinformatics : a theoretical and practical approach /
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作 者：edited by Stephen A. Krawetz and David D. Womble.
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ISBN：9781588292414
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简介
Summary:
Publisher Summary 1
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.
目录
Preface p. v
Contributors p. xi
Part I. Biochemistry, Cell, and Molecular Biology
A. The Cell
1 Nucleic Acids and Proteins: Modern Linguistics for the Genomics and Bioinformatics Era Bradley C. Hyman p. 5
2 Structure and Function of Cell Organelles Jon Holy p. 25
3 Cell Signaling Daniel A. Rappolee p. 55
B. Transcription and Translation
4 DNA Replication, Repair, and Recombination Linda B. Bloom p. 75
5 Transcription, RNA Processing, and Translation Thomas P. Yang and Thomas W. O'Brien p. 93
Part II. Molecular Genetics
A. Genomics
6 Epigenetic Mechanisms Regulating Gene Expression John R. McCarrey p. 123
7 Gene Families and Evolution Ben F. Koop p. 141
8 Repetitive DNA: Detection, Annotation, and Analysis Jerzy Jurka p. 151
9 Molecular Genetics of Disease and the Human Genome Project Paromita Deb-Rinker and Stephen W. Scherer p. 169
B. Clinical Human Genetics
10 Heredity C. A. Rupar p. 187
11 The Clinical Genetics Databases Peter J. Bridge p. 199
12 Population Genetics Jill S. Barnholtz-Sloan p. 207
Part III. The UNIX Operating System
A. Basics and Installation
13 Introduction to UNIX for Biologists David D. Womble p. 233
14 Installation of the Sun Solaris Operating Environment Bryon Campbell p. 247
15 Sun System Administration Bryon Campbell p. 263
B. Managing Bioinformatics Tools
16 Installing Bioinformatics Software in a Server-Based Computing Environment Brian Fristensky p. 285
17 Management of a Server-Based Bioinformatics Resource Brian Fristensky p. 297
C. Command Line Sequence Analysis
18 GCG File Management Sittichoke Saisanit p. 309
19 GCG Sequence Analysis Sittichoke Saisanit p. 315
Part IV. Computer Applications
A. Management and Analysis of DNA Sequencing Projects and Sequences
20 Managing Sequencing Projects in the GAP4 Environment Rodger Staden and David P. Judge and James K. Bonfield p. 327
21 OLIGO Primer Analysis Software John D. Offerman and Wojciech Rychlik p. 345
22 Statistical Modeling of DNA Sequences and Patterns Gautam B. Singh p. 357
23 Statistical Mining of the Matrix Attachment Regions in Genomic Sequences Gautam B. Singh p. 375
24 Analyzing Sequences Using the Staden Package and EMBOSS Rodger Staden and David P. Judge and James K. Bonfield p. 393
B. The Genome Database: Analysis and Similarity Searching
25 Ensembl: An Open-Source Software Tool for Large-Scale Genome Analysis James W. Stalker and Anthony V. Cox p. 413
26 The PIR for Functional Genomics and Proteomics Cathy H. Wu p. 431
27 Sequence Similarity and Database Searching David S. Wishart p. 443
28 GCG Database Searching David J. Heard p. 463
C. Identifying Functional and Structural Sequence Elements
29 Pattern Discovery: Methods and Software Brona Brejova and Tomas Vinar and Ming Li p. 491
30 The Role of Transcription Factor Binding Sites in Promoters and Their In Silico Detection Thomas Werner p. 523
31 An Introduction to Multiple Sequence Alignment and Analysis Steven M. Thompson p. 539
32 3D Molecular Visualization with Protein Explorer Eric Martz p. 565
33 Multiple Sequence Alignment and Analysis: The SeqLab Interface: A Practical Guide Steven M. Thompson p. 587
D. Analysis of Gene Expression: Microarrays and Other Tools
34 Overview of the Tools for Microarray Analysis: Transcription Profiling, DNA Chips, and Differential Display Jeffrey A. Kramer p. 637
35 Microarrays: Tools for Gene Expression Analysis Sorin Draghici p. 665
36 Knowledge Discovery from the Human Transcriptome Kousaku Okubo and Teruyoshi Hishiki p. 693
Part V. Appendices
Appendix 1 CD Contents p. 715
Appendix 2 A Collection of Useful Bioinformatic Tools and Molecular Tables p. 719
Appendix 3 Simple UNIX Commands p. 723
Index p. 725
Contributors p. xi
Part I. Biochemistry, Cell, and Molecular Biology
A. The Cell
1 Nucleic Acids and Proteins: Modern Linguistics for the Genomics and Bioinformatics Era Bradley C. Hyman p. 5
2 Structure and Function of Cell Organelles Jon Holy p. 25
3 Cell Signaling Daniel A. Rappolee p. 55
B. Transcription and Translation
4 DNA Replication, Repair, and Recombination Linda B. Bloom p. 75
5 Transcription, RNA Processing, and Translation Thomas P. Yang and Thomas W. O'Brien p. 93
Part II. Molecular Genetics
A. Genomics
6 Epigenetic Mechanisms Regulating Gene Expression John R. McCarrey p. 123
7 Gene Families and Evolution Ben F. Koop p. 141
8 Repetitive DNA: Detection, Annotation, and Analysis Jerzy Jurka p. 151
9 Molecular Genetics of Disease and the Human Genome Project Paromita Deb-Rinker and Stephen W. Scherer p. 169
B. Clinical Human Genetics
10 Heredity C. A. Rupar p. 187
11 The Clinical Genetics Databases Peter J. Bridge p. 199
12 Population Genetics Jill S. Barnholtz-Sloan p. 207
Part III. The UNIX Operating System
A. Basics and Installation
13 Introduction to UNIX for Biologists David D. Womble p. 233
14 Installation of the Sun Solaris Operating Environment Bryon Campbell p. 247
15 Sun System Administration Bryon Campbell p. 263
B. Managing Bioinformatics Tools
16 Installing Bioinformatics Software in a Server-Based Computing Environment Brian Fristensky p. 285
17 Management of a Server-Based Bioinformatics Resource Brian Fristensky p. 297
C. Command Line Sequence Analysis
18 GCG File Management Sittichoke Saisanit p. 309
19 GCG Sequence Analysis Sittichoke Saisanit p. 315
Part IV. Computer Applications
A. Management and Analysis of DNA Sequencing Projects and Sequences
20 Managing Sequencing Projects in the GAP4 Environment Rodger Staden and David P. Judge and James K. Bonfield p. 327
21 OLIGO Primer Analysis Software John D. Offerman and Wojciech Rychlik p. 345
22 Statistical Modeling of DNA Sequences and Patterns Gautam B. Singh p. 357
23 Statistical Mining of the Matrix Attachment Regions in Genomic Sequences Gautam B. Singh p. 375
24 Analyzing Sequences Using the Staden Package and EMBOSS Rodger Staden and David P. Judge and James K. Bonfield p. 393
B. The Genome Database: Analysis and Similarity Searching
25 Ensembl: An Open-Source Software Tool for Large-Scale Genome Analysis James W. Stalker and Anthony V. Cox p. 413
26 The PIR for Functional Genomics and Proteomics Cathy H. Wu p. 431
27 Sequence Similarity and Database Searching David S. Wishart p. 443
28 GCG Database Searching David J. Heard p. 463
C. Identifying Functional and Structural Sequence Elements
29 Pattern Discovery: Methods and Software Brona Brejova and Tomas Vinar and Ming Li p. 491
30 The Role of Transcription Factor Binding Sites in Promoters and Their In Silico Detection Thomas Werner p. 523
31 An Introduction to Multiple Sequence Alignment and Analysis Steven M. Thompson p. 539
32 3D Molecular Visualization with Protein Explorer Eric Martz p. 565
33 Multiple Sequence Alignment and Analysis: The SeqLab Interface: A Practical Guide Steven M. Thompson p. 587
D. Analysis of Gene Expression: Microarrays and Other Tools
34 Overview of the Tools for Microarray Analysis: Transcription Profiling, DNA Chips, and Differential Display Jeffrey A. Kramer p. 637
35 Microarrays: Tools for Gene Expression Analysis Sorin Draghici p. 665
36 Knowledge Discovery from the Human Transcriptome Kousaku Okubo and Teruyoshi Hishiki p. 693
Part V. Appendices
Appendix 1 CD Contents p. 715
Appendix 2 A Collection of Useful Bioinformatic Tools and Molecular Tables p. 719
Appendix 3 Simple UNIX Commands p. 723
Index p. 725
Introduction to bioinformatics : a theoretical and practical approach /
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