Sequence Analysis in a Nutshell

Pulls together all of the vital information about the most commonly used databases, analytical tools, and tables used in sequence analysis. Contains details and examples of the common database formats (GenBank, EMBL, SWISS-PROT) and the GenBank/EMBL/DDBJ Feature Table Definitions. Also provides the command line syntax for popular analysis applications such as Readseq and MEME/MAST, BLAST, ClustalW, and the EMBOSS suite, as well as tables of nucleotide, genetic, and amino acid codes. Written in O'Reilly's popular, straightforward "Nutshell" format.

Preface 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 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 III. Appendixes A. Nucleotide and Amino Acid Tables B. Genetic Codes C. Resources D. Future Plans Index