Bioinformatics Methods and Protocols

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Stephen Misener, Stephen A. Krawetz
Springer Science & Business Media, 1999 - Computers - 500 pages
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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.
 

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Contents

GCG The Wisconsin Package of Sequence Analysis Programs
3
WebBased Interfaces for the GCG Sequence Analysis Programs
23
Omiga A PCBased Sequence Analysis Tool
31
MacVector Integrated Sequence Analysis for the Macintosh
47
DNASTARs Lasergene Sequence Analysis Software
71
PepTool and GeneTool PlatformIndependent Tools for Biological Sequence Analysis
93
The Staden Package 1998
115
Building a Multiuser Sequence Analysis Facility Using Freeware
131
The NCBI Publicly Available Tools and Resources on the Web
301
Resources at EBI
313
ComputerAssisted Analysis of Transcription Control Regions MatInspector and Other Programs Thomas Werner
337
Computational Approaches for Gene Identification
351
Primer3 on the WWW for General Users and for Biologist Programmers
365
Using the WWW to Supply the Molecular Biology Lab
387
COMPUTERS AND MOLECULAR BIOLOGY ISSUES AND CONSTRAINTS
399
Network Computing Restructuring How Scientists Use Computers and What We Get Out of Them
401

MOLECULAR BIOLOGY SOFTWARE
147
Free Software in Molecular Biology for Macintosh and MS Windows Computers
149
Software Listings
157
Flexible Sequence Similarity Searching with the FASTA3 Program Package William R Pearson 1 Introduction
185
The Use of CLUSTAL W and CLUSTAL X for Multiple Sequence Alignment
221
Phylogenetic Analysis Using PHYLIP
243
Annotating Sequence Data Using Genotator
259
Low Cost Gel Analysis
277
WEBBASED RESOURCES
289
Computer Resources for the Clinical and Molecular Geneticist
291
Computing with DNA
413
Detecting Biological Patterns The Integration of Databases Models and Algorithms
431
TEACHING BIOINFORMATICS AND KEEPING UPTODATE WITH THE LITERATURE
447
Design and Implementation of an Introductory Course for Computer Applications in Molecular Biology and Genetics
449
The Virtual Library I
461
The Virtual Library II
471
The Virtual Library III
481
Index
491
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