Description
Book SynopsisGene 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. This is a resource for anyone who needs to know about the practical aspects and mechanics of sequence analysis.
Table of ContentsPreface 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
