Publisher: O'Reilly, 2003, 286 pages
Keywords: Databases, Programming
Wish you knew which EMBOSS program to use for finding restriction enzyme sites in DNA? Can't remember where you saw that list of BLAST command-line options? Wish you could remember the difference between the polyA site and polyA signal features in GenBank? The answers to these and many other questions about the tools and databases used in sequence analysis are here in this book.
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases pulls together essential information to help you use the popular databases, analytical tools, and tables available for gene sequence analysis. This book contains examples of flat files from key databases (GenBank, EMBL, DDBJ, Pfam, PROSITE, and 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. Detailed information on nucleotide, protein, and genetic codes is also provided. Finally, this volume details command-line syntax for the most popular sequence analysis applications: Readseq, MEME/MAST, BLAST, ClustalW, HMMER, BLAT, and the EMBOSS suite of analytical tools.
Whether you're a student or a bioinformatician in industry or academia, if sequence analysis is part of your daily life, you'll want this easy-to-use reference on your desk.
First of all, this is in the wrong category. This is about some applications that are used in biochemical sequencing. A very limited audience, but for those, a very good book.
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