Introduction to Bioinformatics

Introduction to Bioinformatics : A Theoretical And Practical Approach

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to Bioinformatics A Theoretical and Practical Approach Edited by Stephen A. Krawetz, PhD Wayne State University School of Medicine, Detroit MI and David D. Womble, PhD Wayne State University School of Medicine, Detroit, MI ~ Springer Science+ ~ Business Media, LLC (c) 2003 Springer Science+Business Media New York Originally published by Humana Press !ne. in 2003 Softcover reprint of the hardcover 1 st edition 2003 Ali rights reserved. No part of this book may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording, or otherwise without written permission from the Publisher. Ali papers, comments, opinions, conclusions, or recommendations are those of the author(s), and do not necessarily reflect the views of the publisher. This publication is printed on acid-free paper. G) ANSI Z39.48-1984 (American Standards Institute) Permanence of Paper for Printed Library Materials. Production Editor: Mark J. Breaugh. Cover design by Patricia F. Cleary and Paul A. Thiessen. Cover illustration by Paul A. Thiessen,
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Product details

  • Hardback | 746 pages
  • 153.4 x 281.4 x 25.9mm | 889.06g
  • Humana Press Inc.
  • Totowa, NJ, United States
  • English
  • 2003 ed.
  • XII, 746 p.
  • 1588290646
  • 9781588290649

Back cover copy

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.
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.
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Review quote

"...contains very valuable information on a wide range of topics related to bioinformatics research." - Heredity
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Table of contents

Part I. Biochemistry, Cell, and Molecular Biology

A. The Cell

Nucleic Acids and Proteins: Modern Linguistics for the Genomics and Bioinformatics Era

Bradley C. Hyman

Structure and Function of Cell Organelles

Jon Holy

Cell Signaling

Daniel A. Rappolee

B. Transcription and Translation

DNA Replication, Repair, and Recombination

Linda B. Bloom

Transcription, RNA Processing, and Translation

Thomas P. Yang and Thomas W. O'Brien

Part II. Molecular Genetics

A. Genomics

Epigenetic Mechanisms Regulating Gene Expression

John R. McCarrey

Gene Families and Evolution

Ben F. Koop

Repetitive DNA: Detection, Annotation, and Analysis

Jerzy Jurka

Molecular Genetics of Disease and the Human Genome Project

Paromita Deb-Rinker and Stephen W. Scherer

B. Clinical Human Genetics


C. A. Rupar

The Clinical Genetics Databases

Peter J. Bridge

Population Genetics

Jill S. Barnholtz-Sloan

Part III. The UNIX Operating System

A. Basics and Installation

Introduction to UNIX for Biologists

David D. Womble

Installation of the Sun Solaris (TM) 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

Statistical Mining of the Matrix Attachment Regions in Genomic Sequences

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

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

The Role of Transcription Factor Binding Sites in Promoters and Their In Silico Detection

Thomas Werner

An Introduction to Multiple Sequence Alignment and Analysis

Steven M. Thompson

3D Molecular Visualization with Protein Explorer

Eric Martz

Multiple Sequence Alignment and Analysis: The SeqLab Interface: A Practical Guide

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

Part V. Appendices

Appendix 1: CD Contents

Appendix 2: A Collection of Useful Bioinformatic Tools and Molecular Tables

Appendix 3: Simple UNIX Commands

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