Introduction to Bioinformatics A Theoretical and Practical Approach

About this book

Introductory text for the undergraduate, graduate, or professional. This text provides scientists with both a biological framework to understand the questions life scientists 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.

Contents

Contents Part I. Biochemistry, Cell and Molecular Biology A. The Cell Structure and Function of Cell Organelles Jon Holy Cell Signaling Daniel A. Rappolee Nucleic Acids and Proteins Bradley C. Hyman B. Transcription and Translation Transcription, RNA Processing, and Translation Thomas P. Yang and Thomas W. O'Brien The Role of Transcription Factor-Binding Sites in Promoters and Their in silico Detection Thomas Werner Part II. Molecular Genetics A. Regulating the Genome Epigenetic Mechanisms Regulating Gene Expression John R. McCarrey Statistical Mining of the Matrix Attachment Regions in Genomic Sequences Gautam B. Singh Molecular Genetics of Disease and the Human Genome Project Stephen W. Scherer and Paromita Deb-Rinker DNA Replication, Repair, and Recombination Linda B. Bloom B. Clinical Human Genetics Heredity C. A. Rupar The Clinical Genetics Databases Peter J. Bridge Population Genetics Jill S. Barnholtz-Sloan Part III. The Unix Operating System A. Installation Installation of the SUN Solaris' Operating Environment Bryon Campbell SUN System Administration Bryon Campbell B. Managing Bioinformatics Tools Installing Bioinformatics Software in a Server-Based Computing Environment Brian Fristensky Management of a Server-Based Bioinformatics Resource Brian Fristensky C. Command Line Sequence Analysis GCG File Management Sittichoke Saisanit GCG Sequence Analysis Sittichoke Saisanit Part IV. Computer Applications A. Management and Analysis of DNA Sequencing Projects and Sequences Managing Sequencing Projects in the GAP4 Environment Rodger Staden, David P. Judge, and James K. Bonfield OLIGO Primer Analysis Software John D. Offerman and Wojciech Rychlik Statistical Modeling of DNA Sequences and Patterns Gautam B. Singh Analyzing Sequences Using the Staden Package and EMBOSS Rodger Staden, David P. Judge, and James K. Bonfield B. The Genome Database: Analysis and Similarity Searching Ensembl: An Open-Source Software Tool for Large-Scale Genome Analysis James W. Stalker and Anthony V. Cox Repetitive DNA: Detection, Annotation, and Analysis Jerzy Jurka The PIR for Functional Genomics and Proteomics Cathy H. Wu Sequence Similarity and Database Searching David S. Wishart GCG Database Searching David J. Heard C. Identifying Functional and Structural Sequence Elements Pattern Discovery: Methods and Software Brona Brejova, Tomas Vinar, and Ming Li An Introduction to Multiple Sequence Alignment and Analysis Steven M. Thompson 3-D Molecular Visualization with Protein Explorer Eric Martz Gene Families and Evolution Ben F. Koop Multiple Sequence Alignment and Analysis: The SeqLab Interface 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 Jeffrey A. Kramer Microarrays: Tools for Gene Expression Analysis Sorin Draghici Knowledge Discovery from the Human Transcriptome Kousaku Okubo and Teruyoshi Hishiki

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