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BLAST

by Joseph Bedell Ian Korf Mark Yandell

BLAST (Basic Local Alignment Search Tool) is a set of similarity search programs that explore all of the available sequence databases for protein or DNA. BLAST is the only book completely devoted to this popular and important technology and offers biologists, computational biology students, and bioinformatics professionals a clear understanding of this program. This book shows you how to get specific answers with BLAST and how to use the software to interpret results. If you have an interest in sequence ana

BLAST

by Joseph Bedell Ian Korf Mark Yandell

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.

Unix and Perl to the Rescue!

by Ian Korf Keith Bradnam

Your research has generated gigabytes of data and now you need to analyse it. You hate using spreadsheets but it is all you know, so what else can you do? This book will transform how you work with large and complex data sets, teaching you powerful programming tools for slicing and dicing data to suit your needs. Written in a fun and accessible style, this step-by-step guide will inspire and inform non-programmers about the essential aspects of Unix and Perl. It shows how, with just a little programming knowledge, you can write programs that could save you hours, or even days. No prior experience is required and new concepts are introduced using numerous code examples that you can try out for yourself. Going beyond the basics, the authors touch upon many broader topics that will help those new to programming, including debugging and how to write in a good programming style.

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