Bioinformatics Methods and Protocols

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.

Klappentext

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.

Zusammenfassung
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.

Inhalt
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.