Introduction to bioinformatics : a theoretical and practical approach / edited by Stephen A. Krawetz and David D. Womble.

Format:

Book

Contributor:

Krawetz, Stephen A.

Womble, David D.

Language:

English

Subjects (All):

Bioinformatics.

Computational Biology--methods.

Computer Systems.

Databases, Genetic.

Genomics.

Sequence Analysis, DNA.

Software.

Medical Subjects:

Computational Biology--methods.

Computer Systems.

Databases, Genetic.

Genomics.

Sequence Analysis, DNA.

Software.

Physical Description:

xii, 746 pages : illustrations ; 26 cm + 1 CD-ROM (4 3/4 in.)

4 3/4 in.

Place of Publication:

Totowa, N.J. : Humana Press, 2003.

System Details:

System requirements for accompanying CD-ROM: IBM-compatible PC or Macintosh; Adobe Acrobat Reader 4.0 or later; CD-ROM drive.

text file

Summary:

The genomic revolution that has spawned microarrays and high throughput technologies has produced vast amounts of complex biological data that require integration and multidimensional analysis. In Introduction to Bioinformatics: A Theoretical and Practical Approach, leading researchers and experts introduce the key biological, mathematical, statistical, and computer concepts and tools necessary for physical and life scientists to understand and analyze these data.

For physical and computer scientists, the book provides a sound biological framework for understanding the questions a life scientist would ask in the context of currently available computational tools. Here, the basic cellular structure and the biological decoding of the genome, the long-range regulation of the genome, the in silico detection of the elements that impact long-range control, and the molecular genetic basis of disease as a consequence of replication are explained. Reviews of clinical human genetics, the various clinical databases, and pertinent issues in population genetics complete this tutorial.

For life scientists, a complete discussion of the UNIX operating system, which is commonly used to support advanced computational tools, offers biologists graphical-user-interface comfort in a command-line environment, plus an understanding of the installation and management of UNIX-based software tools.

It is in the applications sections that the book provides a common meeting ground for life and physical scientists. Here they will find examples of the management and analysis of DNA sequencing projects, the modeling of DNA as a statistical series of patterns, various methods of pattern discovery, protein visualization, and the use of multiple sequence alignment to infer both functional and structural biological relationships. An accompanying CD contains several full and limited-trial versions of the programs discussed in the text, as well as a complete set of illustrations from each chapter specifically prepared for use as illustrative instructional material for lectures and presentations.

Cross-disciplinary and highly instructive, Introduction to Bioinformatics: A Theoretical and Practical Approach offers life, mathematical, computer, and statistical scientists an integrated foundation for using today's many new computational advances to elucidate the nuances of both genetic code and integrated biological systems.

Contents:

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 5

2 Structure and Function of Cell Organelles / Jon Holy 25

3 Cell Signaling / Daniel A. Rappolee 55

B. Transcription and Translation

4 DNA Replication, Repair, and Recombination / Linda B. Bloom 75

5 Transcription, RNA Processing, and Translation / Thomas P. Yang, Thomas W. O'Brien 93

Part II. Molecular Genetics

A. Genomics

6 Epigenetic Mechanisms Regulating Gene Expression / John R. McCarrey 123

7 Gene Families and Evolution / Ben F. Koop 141

8 Repetitive DNA: Detection, Annotation, and Analysis / Jerzy Jurka 151

9 Molecular Genetics of Disease and the Human Genome Project / Paromita Deb-Rinker, Stephen W. Scherer 169

B. Clinical Human Genetics

10 Heredity / C. A. Rupar 187

11 The Clinical Genetics Databases / Peter J. Bridge 199

12 Population Genetics / Jill S. Barnholtz-Sloan 207

Part III. The UNIX Operating System

A. Basics and Installation

13 Introduction to UNIX for Biologists / David D. Womble 233

14 Installation of the Sun Solaris Operating Environment / Bryon Campbell 247

15 Sun System Administration / Bryon Campbell 263

B. Managing Bioinformatics Tools

16 Installing Bioinformatics Software in a Server-Based Computing Environment / Brian Fristensky 285

17 Management of a Server-Based Bioinformatics Resource / Brian Fristensky 297

C. Command Line Sequence Analysis

18 GCG File Management / Sittichoke Saisanit 309

19 GCG Sequence Analysis / Sittichoke Saisanit 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, David P. Judge, James K. Bonfield 327

21 OLIGO Primer Analysis Software / John D. Offerman, Wojciech Rychlik 345

22 Statistical Modeling of DNA Sequences and Patterns / Gautam B. Singh 357

23 Statistical Mining of the Matrix Attachment Regions in Genomic Sequences / Gautam B. Singh 375

24 Analyzing Sequences Using the Staden Package and EMBOSS / Rodger Staden, David P. Judge, James K. Bonfield 393

B. The Genome Database: Analysis and Similarity Searching

25 Ensembl: An Open-Source Software Tool for Large-Scale Genome Analysis / James W. Stalker, Anthony V. Cox 413

26 The PIR for Functional Genomics and Proteomics / Cathy H. Wu 431

27 Sequence Similarity and Database Searching / David S. Wishart 443

28 GCG Database Searching / David J. Heard 463

C. Identifying Functional and Structural Sequence Elements

29 Pattern Discovery: Methods and Software / Brona Brejova, Tomas Vinar, Ming Li 491

30 The Role of Transcription Factor Binding Sites in Promoters and Their In Silico Detection / Thomas Werner 523

31 An Introduction to Multiple Sequence Alignment and Analysis / Steven M. Thompson 539

32 3D Molecular Visualization with Protein Explorer / Eric Martz 565

33 Multiple Sequence Alignment and Analysis: The SeqLab Interface: A Practical Guide / Steven M. Thompson 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 637

35 Microarrays: Tools for Gene Expression Analysis / Sorin Draghici 665

36 Knowledge Discovery from the Human Transcriptome / Kousaku Okubo, Teruyoshi Hishiki 693.

Notes:

Includes bibliographical references and index.

ISBN:

1588290646

158829241X

OCLC:

48958471