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Bioinformatics Methods and Protocols

  • Book
  • © 1999

Overview

Editors:
  1. Stephen Misener

    1. Queen’s University, Kingston, Canada

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  2. Stephen A. Krawetz

    1. Wayne State University, Detroit

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

Part of the book series: Methods in Molecular Biology (MIMB, volume 132)

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Table of contents (28 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Sequence Analysis Packages

    1. Front Matter

      Pages 1-1
      Download chapter PDF

    2. GCG:

      • David D. Womble
      Pages 3-22

    3. Web-Based Interfaces for the GCG Sequence Analysis Programs

      • David D. Womble
      Pages 23-30

    4. Omiga

      • Jeffrey A. Kramer
      Pages 31-45

    5. MacVector

      • Promila A. Rastogi
      Pages 47-69

    6. DNASTAR’s Lasergene Sequence Analysis Software

      • Timothy G. Burland
      Pages 71-91

    7. PepTool™ and GeneTool™:

      • David S. Wishart, Paul Stothard, Gary H. Van Domselaar
      Pages 93-113

    8. The Staden Package, 1998

      • Rodger Staden, Kathryn F. Beal, James K. Bonfield
      Pages 115-130

    9. Building a Multiuser Sequence Analysis Facility Using Freeware

      • Brian Fristensky
      Pages 131-145

  3. Molecular Biology Software

    1. Front Matter

      Pages 147-147
      Download chapter PDF

    2. Free Software in Molecular Biology for Macintosh and MS Windows Computers

      • Don Gilbert
      Pages 149-184

    3. Flexible Sequence Similarity Searching with the FASTA3 Program Package

      • William R. Pearson
      Pages 185-219

    4. The Use of CLUSTAL W and CLUSTAL X for Multiple Sequence Alignment

      • Ashok Aiyar
      Pages 221-241

    5. Phylogenetic Analysis Using PHYLIP

      • Jacques D. Retief
      Pages 243-258

    6. Annotating Sequence Data Using Genotator

      • Nomi L. Harris
      Pages 259-276

    7. Low Cost Gel Analysis

      • Jeffry A. Reidler
      Pages 277-288

  4. Web-Based Resources

    1. Front Matter

      Pages 289-289
      Download chapter PDF

    2. Computer Resources for the Clinical and Molecular Geneticist

      • Yuval Yaron, Avi Orr-Urtreger
      Pages 291-299

    3. The NCBI

      • Jack P. Jenuth
      Pages 301-312
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About this book

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 Protocols 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 Protocols 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.

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 Protocols; 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 Protocols 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

Editors and Affiliations

  • Queen’s University, Kingston, Canada

    Stephen Misener

  • Wayne State University, Detroit

    Stephen A. Krawetz

Bibliographic Information

  • Book Title: Bioinformatics Methods and Protocols

  • Editors: Stephen Misener, Stephen A. Krawetz

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1385/1592591922

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Humana Press 1999

  • Hardcover ISBN: 978-0-89603-732-8Published: 26 August 1999

  • Softcover ISBN: 978-1-61737-156-1Published: 10 November 2010

  • eBook ISBN: 978-1-59259-192-3Published: 02 February 2008

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 500

  • Topics: Cell Biology

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