Bioinformatics Methods and Protocols / Edition 1

by Stephen Misener, Stephen A. Krawetz

Overview

Computers have become an essential component of modern biology. They help to manage the vast and increasing amount of biological data and continue to play an integral role in the discovery of new biological relationships. This in silico approach to biology has helped to reshape the modern biological sciences. With the biological revolution now among us, it is imperative that each scientist develop and hone today’s bioinformatics skills, if only at a rudimentary level. Bioinformatics Methods and Prools was conceived as part of the Methods in Molecular Biology series to meet this challenge and to provide the experienced user with useful tips and an up-to-date overview of current developments. It builds upon the foundation that was provided in the two-volume set published in 1994 entitled Computer Analysis of Sequence Data. We divided Bioinformatics Methods and Prools into five parts, including a thorough survey of the basic sequence analysis software packages that are available at most institutions, as well as the design and implemen- tion of an essential introductory Bioinformatics course. In addition, we included sections describing specialized noncommercial software, databases, and other resources available as part of the World Wide Web and a stimul- ing discussion of some of the computational challenges biologists now face and likely future solutions.

Product Details

ISBN-13:	9781617371561
Publisher:	Springer-Verlag New York, LLC
Publication date:	11/10/2010
Series:	Methods in Molecular Biology , #132
Edition description:	Softcover reprint of hardcover 1st ed. 1999
Pages:	500
Product dimensions:	5.98(w) x 9.02(h) x 0.35(d)

About the Author

Misener, Stephen (Queen's Univ, Kingston, ON); Krawetz, Stephen A. (Wayne State Univ)

Table of Contents

Sequence Analysis Packages.- GCG:.- Web-Based Interfaces for the GCG Sequence Analysis Programs.- Omiga.- MacVector.- DNASTAR’s Lasergene Sequence Analysis Software.- PepTool™ and GeneTool™:.- The Staden Package, 1998.- Building a Multiuser Sequence Analysis Facility Using Freeware.- Molecular Biology Software.- Free Software in Molecular Biology for Macintosh and MS Windows Computers.- Flexible Sequence Similarity Searching with the FASTA3 Program Package.- The Use of CLUSTAL W and CLUSTAL X for Multiple Sequence Alignment.- Phylogenetic Analysis Using PHYLIP.- Annotating Sequence Data Using Genotator.- Low Cost Gel Analysis.- Web-Based Resources.- Computer Resources for the Clinical and Molecular Geneticist.- The NCBI.- Resources at EBI.- Computer-Assisted Analysis of Transcription Control Regions.- Computational Approaches for Gene Identification.- Primer3 on the WWW for General Users and for Biologist Programmers.- Using the WWW to Supply the Molecular Biology Lab.- Computers and Molecular Biology: Issues and Constraints.- Network Computing.- Computing with DNA.- Detecting Biological Patterns The Integration of Databases, Models, and Algorithms.- Teaching Bioinformatics and Keeping Up-To-Date With the Literature.- Design and Implementation of an Introductory Course for Computer Applications in Molecular Biology and Genetics.- The Virtual Library I.- The Virtual Library II.- The Virtual Library III.

Editorial Reviews

"There has been a need for a book of this kind for some time. It is remarkably complete and could be extremely useful for those laboratories that are thinking seriously about their bioinformatic requirements...The chapters are clearly laid out and the text is generally easy to read and refreshingly free of much of the jargon that can be found in bioinformatics...I would highly recommend it for institutional purchase." -Microbiology Today

"...there are some real gems in Bioinformatics: Methods and Prools; the chapter on phylogenetic analysis presents enough information to produce a tree that one could submit for publication without too much apprehension, and William Pearson's clear and trenchant discussion of his FASTA programs (and the similar BLAST suite) alone might justify the purchase of this book..." -Tibtech

"This book is an interesting mix of the practical and theoretical aspects of bioinformatics, and those readers interested in obtaining information on specific tools and resources will not be disappointed....this book provides a nice overview of a number of different aspects of the field. The focus on inexpensive tools and resources is also likely to be very popular with those scientists new to the field and possibly just starting their careers as independent researchers. Bioinformatics Methods and Prools is an invaluable resource for this target audience. It is a solid introduction to the practical aspects of bioinformatics research." -Biotech Software & Internet Report

"This book gives many details concerning the computational challenges facing biologists and their likely future solutions, cities shareware that can be used to build an analysis suite to meet specific needs, describes software, databases, and other resources available on the www, discusses common image analysis techniques, reviews oligonucleotide and PCR-primer design, serves as an important bioinformatics teaching resource and provides, a tested course design and resource for an introductory graduate level course." - Cellular and Molecular Biology

"It is a useful aid to choosing software, the material on the design of an introductory course will be useful to some, and parts of it will serve as good guides to particular pieces of software." -Biochemistry and Molecular Biology Education

From the Publisher

3 Stars from Doody

This is a compendium of brief descriptions of the many software programs used in studies of DNA and protein sequences, as well as molecular biology software in general. It is one in a series on Methods in Molecular Biology published by Humana Press. This book is intended as a resource for researchers who may not be familiar with all the software available to support this kind of research. It is not clear to me that researchers in these fields would need a book like this to find appropriate software. Nonetheless, the book does provide the information described by the editors. This book would be of use only to researchers who already rely on one or more of the software packages described. The several authors of the various chapters appear to be knowledgeable in their respective topics. The content of the book is almost entirely a list and brief description of software for DNA and protein sequence analysis and molecular biology techniques that can be loaded on individual computers or accessed via the World Wide Web. The book includes a discussion of issues and applications of the software as potential research tools themselves. There is also a short section on what might be included in a course on bioinformatics. This book may be useful to some researchers, but most who are active in these fields would be familiar with most, if not all, of the software packages described. Furthermore, the software changes so rapidly and all of them are available through various national resources and data banks, so it is not clear who would actually need a book like this. It may turn out that the value of this book will reside in its historical or archival content as it much as its use as a currentresearch resource.

Alvin Telser

Users and veterans survey the key biological software packages available and offer tips and an overview of the current development in the resources. Among the sequence analysis systems they review are GCG, Omiga, MacVector, DNASTAR, PepTool, GeneTool, and the Staden Package. Those for molecular biology include Genotator and sequence- similarity searching using FASTA, CLUSAL multiple sequence alignment, and phylogenetic analysis. They discuss Web-based resources such as primary sequence databases, primary sequence analysis methods, and clinical databases useful in molecular medicine. They also outline an introductory course in bioinformatics and suggest ways to keep it current. Annotation c. Book News, Inc., Portland, OR (booknews.com)

Booknews

Reviewer: Alvin Telser, PhD (Northwestern University Feinberg School of Medicine)
Description: This is a compendium of brief descriptions of the many software programs used in studies of DNA and protein sequences, as well as molecular biology software in general. It is one in a series on Methods in Molecular Biology published by Humana Press.
Purpose: This book is intended as a resource for researchers who may not be familiar with all the software available to support this kind of research. It is not clear to me that researchers in these fields would need a book like this to find appropriate software. Nonetheless, the book does provide the information described by the editors.
Audience: This book would be of use only to researchers who already rely on one or more of the software packages described. The several authors of the various chapters appear to be knowledgeable in their respective topics.
Features: The content of the book is almost entirely a list and brief description of software for DNA and protein sequence analysis and molecular biology techniques that can be loaded on individual computers or accessed via the World Wide Web. The book includes a discussion of issues and applications of the software as potential research tools themselves. There is also a short section on what might be included in a course on bioinformatics.
Assessment: This book may be useful to some researchers, but most who are active in these fields would be familiar with most, if not all, of the software packages described. Furthermore, the software changes so rapidly and all of them are available through various national resources and data banks, so it is not clear who would actually need a book like this. It may turn out that the value of this book will reside in its historical or archival content as it much as its use as a current research resource.

Doody's Review Service