Description
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(TM), GeneTool(TM), and the Staden Package. Molecular biology software includes Genotator and sequence-similarity searching using FASTA, CLUSTAL multiple sequence alignment, and phylogenetic analysis. Web-based resources are examined for primary sequence databases, primary sequence analysis methods, and clinical databases useful in molecular medicine. Numerous illustrative examples to teach the reader how to solve problems are included. Bioinformatics: Methods and Protocols 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. 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(TM) and GeneTool(TM): 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-Tom 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 and Helen 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
