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EMBOSS: dbigcg |
A GCG-format database consists of *.seq and *.ref files - only the *.seq files are used. The data in these is often compressed.
The resulting index-file format is used by the software on the EMBL database CD-ROM distribution and by the Staden package in addition to EMBOSS, and appears to be the most generally used and publicly available index file format for these databases.
% dbigcg EMBL : EMBL SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew GB : Genbank, DDBJ PIR : NBRF Entry format [EMBL]: Database name: tembl Database directory [.]: /nfs/disk42/pmr/emboss/test/gcgembl/ Wildcard database filename [*.seq]: Release number [0.0]: Index date [00/00/00]: 04/02/00
Mandatory qualifiers (* if not always prompted): -idformat list Entry format [-dbname] string Database name * -directory string Database directory * -filename string Wildcard database filename -release string Release number -date string Index date Optional qualifiers: (none) Advanced qualifiers: -staden bool Use staden index file names -indexdirectory string Index directory -sortoptions string Sort options, typically '-T .' to use current directory for work files and '-k 1,1' to force GNU sort to use the first field -[no]systemsort bool Use system sort utility -[no]cleanup bool Clean up temporary files General qualifiers: -help bool report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
-idformat | Entry format |
|
EMBL | ||||||||
[-dbname] (Parameter 1) |
Database name | A string from 1 to 19 characters | Required | ||||||||
-directory | Database directory | Any string is accepted | . | ||||||||
-filename | Wildcard database filename | Any string is accepted | *.seq | ||||||||
-release | Release number | A string up to 9 characters | 0.0 | ||||||||
-date | Index date | Date string dd/mm/yy | 00/00/00 | ||||||||
Optional qualifiers | Allowed values | Default | |||||||||
(none) | |||||||||||
Advanced qualifiers | Allowed values | Default | |||||||||
-staden | Use staden index file names | Yes/No | No | ||||||||
-indexdirectory | Index directory | Any string is accepted | . | ||||||||
-sortoptions | Sort options, typically '-T .' to use current directory for work files and '-k 1,1' to force GNU sort to use the first field | Any string is accepted | -T . -k 1,1 | ||||||||
-[no]systemsort | Use system sort utility | Yes/No | Yes | ||||||||
-[no]cleanup | Clean up temporary files | Yes/No | Yes |
Program name | Description |
---|---|
dbiblast | Index a BLAST database |
dbifasta | Index a fasta database |
dbiflat | Index a flat file database |