Bioinformatics Methods and Protocols

"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

• 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.