Introduction to Bioinformatics
A Theoretical And Practical Approach
Samenvatting
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 © 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.
Specificaties
Inhoudsopgave
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
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