Table Of Contents
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
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