Introduction to Bioinformatics: A Theoretical and Practical Approach

ISBN-13: 9781588290649 / Angielski / Twarda / 2003 / 746 str.

Stephen A. Krawetz; David D. Womble

Opis

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 humanapress.com 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, chemicalgraphics.com.

Recenzje

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

Spis treści

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 Heredity 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™ 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 Brejová, Tomás 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 Index

Blurb

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.