BLAST

£22.80

Ian Korf,Mark Yandell and Joseph Bedell; ISBN: 0-596-00299-8

Sequence similarity is a powerful tool for discovering biological function. Just as the ancient Greeks used comparative anatomy to understand the human body and linguists used the Rosetta stone to decipher Egyptian hieroglyphs, today we can use comparative sequence analysis to understand genomes. BLAST (Basic Local Alignment Search Tool), is a sophisticated software package for rapid searching of nucleotide and protein databases. It is one of the most important software packages used in sequence analysis and bioinformatics. Most users of BLAST, however, seldom move beyond the program's default parameters, and never take advantage of its full power.

BLAST is the only book completely devoted to this popular suite of tools. It offers biologists, computational biology students, and bioinformatics professionals a clear understanding of BLAST as well as the science it supports. This book shows you how to move beyond the default parameters, get specific answers using BLAST, and how to interpret your results. The book also contains tutorial and reference sections covering NCBI-BLAST and WU-BLAST, background material to help you understand the statistics behind BLAST, Perl scripts to help you prepare your data and analyze your results, and a wealth of tips and tricks for configuring BLAST to meet your own research needs. Some of the topics covered include:

• BLAST basics and the NCBI web interface
• How to select appropriate search parameters
• BLAST programs: BLASTN, BLASTP, BLASTX, TBLASTN, TBLASTX, PHI-BLAST, and PSI BLAST
• Detailed BLAST references, including NCBI-BLAST and WU-BLAST
• Understanding biological sequences
• Sequence similarity, homology, scoring matrices, scores, and evolution
• Sequence Alignment
• Calculating BLAST statistics
• Industrial-strength BLAST, including developing applications with Perl and BLAST

BLAST is the only comprehensive reference with detailed, accurate information on optimizing BLAST searches for high-throughput sequence analysis. This is a book that any biologist should own.

Developing Bioinformatics Computer Skills

£19.96

Cynthia Gibas and Per Jambeck; ISBN: 1-56592-664-1

Bioinformatics--the application of computational and analytical methods to biological problems--is a rapidly evolving scientific discipline. Genome sequencing projects are producing vast amounts of biological data for many different organisms, and, increasingly, storing these data in public databases. Such biological databases are growing exponentially, along with the biological literature. It's impossible for even the most zealous researcher to stay on top of necessary information in the field without the aid of computer-based tools. Bioinformatics is all about building these tools.

Developing Bioinformatics Computer Skills is for scientists and students who are learning computational approaches to biology for the first time, as well as for experienced biology researchers who are just starting to use computers to handle their data. The book covers the Unix file system, building tools and databases for bioinformatics, computational approaches to biological problems, an introduction to Perl for bioinformatics, data mining, and data visualization.

Written in a clear, engaging style, Developing Bioinformatics Computer Skills will help biologists develop a structured approach to biological data as well as the tools they'll need to analyze the data.

Mastering Perl for Bioinformatics

£22.80

James Tisdall; ISBN: 0-596-00307-2

Historically, programming hasn't been considered a critical skill for biologists. But now, with access to vast amounts of biological data contained in public databases, programming skills are increasingly in strong demand in biology research and development. Perl, with its highly developed capacities in string handling, text processing, networking, and rapid prototyping, has emerged as the programming language of choice for biological data analysis.

Mastering Perl for Bioinformatics covers the core Perl language and many of its module extensions, presenting them in the context of biological data and problems of pressing interest to the biological community. This book, along with Beginning Perl for Bioinformatics, forms a basic course in Perl programming. This second volume finishes the basic Perl tutorial material (references, complex data structures, object-oriented programming, use of modules--all presented in a biological context) and presents some advanced topics of considerable interest in bioinformatics.

The range of topics covered in Mastering Perl for Bioinformatics prepares the reader for enduring and emerging developments in critical areas of bioinformatics programming such as:

• Gene finding
• String alignment
• Methods of data storage and retrieval (SML and databases)
• Modeling of networks (graphs and Petri nets)
• Graphics (Tk)
• Parallelization
• Interfacing with other programming languages
• Statistics (PDL)
• Protein structure determination
• Biological models of computation (DNA Computers)

Biologists and computer scientists who have conquered the basics of Perl and are ready to move even further in their mastery of this versatile language will appreciate the author's well-balanced approach to applying Perl's analytical abilities to the field of bioinformatics. Full of practical examples and real-world biological problem solving, this book is a must for any reader wanting to move beyond beginner level Perl in bioinformatics.

Sequence Analysis in a Nutshell

£16.76

Scott Markel and Darryl León; ISBN: 0-596-00494-X

Gene sequence data is the most abundant type of data available, and if you're interested in analyzing it, you'll find a wealth of computational methods and tools to help you. In fact, finding the data is not the challenge at all; rather it is dealing with the plethora of flat file formats used to process the sequence entries and trying to remember what their specific field codes mean. If you survive by surrounding yourself with well-thumbed hard copies of readme files or remembering exactly where to look for the details when you need them, then Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases is for you. This book is a handy resource, as well as an invaluable reference, for anyone who needs to know about the practical aspects and mechanics of sequence analysis.

Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases pulls together all of the vital information about the most commonly used databases, analytical tools, and tables used in sequence analysis. The book is partitioned into three fundamental areas to help you maximize your use of the content. The first section, "Databases" contains examples of flatfiles from key databases (GenBank, EMBL, SWISS-PROT), the definitions of the codes or fields used in each database, and the sequence feature types/terms and qualifiers for the nucleotide and protein databases.

The second section, "Tools" provides the command line syntax for popular applications such as ReadSeq, MEME/MAST, BLAST, ClustalW, and the EMBOSS suite of analytical tools. The third section, "Appendixes" concentrates on information essential to understanding the individual components that make up a biological sequence. The tables in this section include nucleotide and protein codes, genetic codes, as well as other relevant information.

Written in O'Reilly's enormously popular, straightforward "Nutshell" format, this book draws together essential information for bioinformaticians in industry and academia, as well as for students. If sequence analysis is part of your daily life, you'll want this easy-to-use book on your desk.