Sequence Analysis in a Nutshell

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.

• Part I: Data Formats
1. FASTA Format
• NCBI's Sequence Identifier Syntax
• NCBI's Non-Redundant Database Syntax
• References
2. GenBank/EMBL/DDBJ
• Example Flat Files
• GenBank Example Flat File
• DDBJ Example Flat File
• GenBank/DDBJ Field Definitions
• EMBL Example Flat File
• EMBL Field Definitions
• DDBJ/EMBL/GenBank Feature Table
• References
3. SWISS-PROT
• SWISS-PROT Example Flat File
• SWISS-PROT Field Definitions
• SWISS-PROT Feature Table
• References
4. Pfam
• Pfam Example Flat File
• Pfam Field Definitions
• References
5. PROSITE
• PROSITE Example Flat File
• PROSITE Field Definitions
• References
• Part II: Tools
6. Readseq
• Supported Formats
• Command-Line Options
• References
7. BLAST
• formatdb
• blastall
• megablast
• blastpgp
• PSI-BLAST
• PHI-BLAST
• bl2seq
• References
8. BLAT
• Command-Line Options
• References
9. ClustalW
• Command-Line options
• References
10. HMMER
• hmmalign
• hmmbuild
• hmmcalibrate
• hmmconvert
• hmmemit
• hmmfetch
• hmmindex
• hmmpfam
• hmmsearch
• References
11. MEME/MAST
• MEME
• MAST
• References
12. EMBOSS
• Common Themes
• List of All EMBOSS Programs
• Details of EMBOSS Programs
• References
• Part III: Appendixes
1. Nucleotide and Mino Acid Tables
2. Genetic Codes
3. Resources
4. Future Plans

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.