Bioinformatics Methods and Protocols

ISBN-13: 9781617371561 / Angielski / Miękka / 2010 / 500 str.

Stephen Misener; Stephen A. Krawetz

Opis

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.

Recenzje

"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

Spis treści

Part 1. Sequence Analysis Packages GCG: The Wisconsin Package of Sequence Analysis Programs David D. Womble Web-Based Interfaces for the GCG Sequence Analysis Programs David D. Womble Omiga: A PC-Based Sequence Analysis Tool Jeffrey A. Kramer MacVector: Integrated Sequence Analysis for the Macintosh Promila A. Rastogi DNASTAR's Lasergene Sequence Analysis Software Timothy G. Burland PepTool™ and GeneTool™: Platform-Independent Tools for Biological Sequence Analysis David S. Wishart, Paul Stothard, and Gary H. Van Domselaar The Staden Package, 1998 Rodger Staden, Kathryn F. Beal, and James K. Bonfield Building a Multiuser Sequence Analysis Facility Using Freeware Brian Fristensky Part 2. Molecular Biology Software Free Software in Molecular Biology for Macintosh and MS Windows Computers Appendix: Software Listings Don Gilbert Flexible Sequence Similarity Searching with the FASTA3 Program Package William R. Pearson The Use of CLUSTAL W and CLUSTAL X for Multiple Sequence Alignment Ashok Aiyar Phylogenetic Analysis Using PHYLIP Jacques D. Retief Annotating Sequence Data Using Genotator Nomi L. Harris Low Cost Gel Analysis Jeffry A. Reidler Part 3. Web-Based Resources Computer Resources for the Clinical and Molecular Geneticist Yuval Yaron and Avi Orr-Urtreger The NCBI: Publicly Available Tools and Resources on the Web Jack P. Jenuth Resources at EBI Patricia Rodriguez-Tomé Computer-Assisted Analysis of Transcription Control Regions: MatInspector and Other Programs Thomas Werner Computational Approaches for Gene Identification Gautam B. Singh Primer3 on the WWW for General Users and for Biologist Programmers Steve Rozen andHelen Skaletsky Using the WWW to Supply the Molecular Biology Lab MaryAnn Labant and Roger Anderson Part 4. Computers and Molecular Biology: Issues and Constraints Network Computing: Restructuring How Scientists Use Computers and What We Get Out of Them Brian Fristensky Computing with DNA Lila Kari and Laura F. Landweber Detecting Biological Patterns: The Integration of Databases, Models, and Algorithms Gautam B. Singh Part 5. 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 Stephen A. Krawetz The Virtual Library I: Searching MEDLINE Keir Reavie The Virtual Library II: Science Citation Index and Current Awareness Services Keir Reavie The Virtual Library III: Electronic Journals, Grants, and Funding Information Keir Reavie

Blurb

In Bioinformatics: Methods and Protocols, hands-on users and experts survey the key biological software packages, offering useful tips and an overview of current developments. Among the sequence analysis systems reviewed are GCG, Omiga, MacVector, DNASTAR, PepTool, GeneTool, and Staden. Molecular biology software includes Genotator and sequence-similarity searching using FASTA, CLUSTAL multiple sequence alignment, and phylogenic analysis. Web-based resources are examined for primary sequence databases, primary sequence analysis methods, and clinical databases useful in molecular medicine. The book also includes a set of guidelines for designing and teaching an introductory bioinformatics course and numerous illustrative examples to teach the reader how to solve problems.

Bioinformatics: Methods and Protocols offers to experienced and novice biologists a broad overview of the computational tools that have reshaped modern biology. It constitutes a gold-standard reference for today's scientists who wish to develop and hone their bioinformatics skills towards the discovery of new biological relationships.