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dbiblast |
The index files of the blast database format are not useful by themselves as they do not hold the entrynames or accession numbers, but they are used as pointers to the reference and sequence information in the database.
Because there are two sequence types (nucleic acid and protein) and two index formats (blast1 from pressdb or setdb, and blast2 from formatdb) with different index file names, dbiblast will ask about the database type. If the answer is "unknown" dbiblast will test each possible set of file names until one is found.
Having created the EMBOSS indices for this file, a database can then be defined in the file emboss.defaults as something like:
DB swnew [ type: P format: embl method: blast directory: /data/embl ]
This creates EMBOSS indices for the BLAST database 'swnew'
% dbiblast Index a BLAST database Database name: swnew Database directory [.]: ../../data Wildcard database filename [swnew]: Release number [0.0]: Index date [00/00/00]: N : nucleic P : protein ? : unknown Sequence type [unknown]: 1 : wublast and setdb/pressdb 2 : formatdb 0 : unknown Blast index version [unknown]: |
Go to the output files for this example
Mandatory qualifiers: [-dbname] string Database name -directory string Database directory -filenames string Wildcard database filename -release string Release number -date string Index date -seqtype menu Sequence type -blastversion menu Blast index version Optional qualifiers: (none) Advanced qualifiers: -fields menu Index fields -exclude string wildcard filename(s) to exclude -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 -maxindex integer Maximum index length -[no]systemsort boolean Use system sort utility -[no]cleanup boolean Clean up temporary files -sourcefile boolean Use FASTA source file General qualifiers: -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |||||||
---|---|---|---|---|---|---|---|---|---|
[-dbname] (Parameter 1) |
Database name | A string from 1 to 19 characters | Required | ||||||
-directory | Database directory | Any string is accepted | . | ||||||
-filenames | Wildcard database filename | Any string is accepted | Database name | ||||||
-release | Release number | A string up to 9 characters | 0.0 | ||||||
-date | Index date | Date string dd/mm/yy | 00/00/00 | ||||||
-seqtype | Sequence type |
|
unknown | ||||||
-blastversion | Blast index version |
|
unknown | ||||||
Optional qualifiers | Allowed values | Default | |||||||
(none) | |||||||||
Advanced qualifiers | Allowed values | Default | |||||||
-fields | Index fields |
|
acnum | ||||||
-exclude | wildcard filename(s) to exclude | Any string is accepted | An empty string is accepted | ||||||
-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 | ||||||
-maxindex | Maximum index length | Integer 0 or more | 0 | ||||||
-[no]systemsort | Use system sort utility | Boolean value Yes/No | Yes | ||||||
-[no]cleanup | Clean up temporary files | Boolean value Yes/No | Yes | ||||||
-sourcefile | Use FASTA source file | Boolean value Yes/No | No |
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dbiblast creates four index files. All are binary but with a simple format.
Program name | Description |
---|---|
dbifasta | Index a fasta database |
dbiflat | Index a flat file database |
dbigcg | Index a GCG formatted database |