|   | dbiblast | 
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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.
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]: 
General log output file [outfile.dbiblast]: 
 | 
Go to the output files for this example
| 
Index a BLAST database
Version: EMBOSS:6.6.0.0
   Standard (Mandatory) qualifiers:
  [-dbname]            string     Database name (Any string from 2 to 19
                                  characters, matching regular expression
                                  /[A-z][A-z0-9_]+/)
   -directory          directory  [.] Database directory
   -filenames          string     [Database name] Wildcard database filename
                                  (Any string)
   -release            string     [0.0] Release number (Any string up to 9
                                  characters)
   -date               string     [00/00/00] Index date (Date string dd/mm/yy)
   -seqtype            menu       [unknown] Sequence type (Values: N
                                  (nucleic); P (protein); ? (unknown))
   -blastversion       menu       [unknown] Blast index version (Values: 1
                                  (wublast and setdb/pressdb); 2 (formatdb); 0
                                  (unknown))
   -outfile            outfile    [*.dbiblast] General log output file
   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -fields             menu       [acc] Index fields (Values: acc (acnum
                                  accession number index); sv (seqvn sequence
                                  version and gi number index); des (des
                                  description index))
   -exclude            string     Wildcard filename(s) to exclude (Any string)
   -sortoptions        string     [-T . -k 1,1] 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)
   -maxindex           integer    [0] Maximum index length (Integer 0 or more)
   -[no]systemsort     boolean    [Y] Use system sort utility
   -[no]cleanup        boolean    [Y] Clean up temporary files
   -sourcefile         boolean    Use FASTA source file
   -indexoutdir        outdir     [.] Index file output directory
   Associated qualifiers:
   "-directory" associated qualifiers
   -extension          string     Default file extension
   "-outfile" associated qualifiers
   -odirectory         string     Output directory
   "-indexoutdir" associated qualifiers
   -extension          string     Default file extension
   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit
 | 
| Qualifier | Type | Description | Allowed values | Default | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||||||||
| [-dbname] (Parameter 1) | string | Database name | Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/ | Required | ||||||
| -directory | directory | Database directory | Directory | . | ||||||
| -filenames | string | Wildcard database filename | Any string | Database name | ||||||
| -release | string | Release number | Any string up to 9 characters | 0.0 | ||||||
| -date | string | Index date | Date string dd/mm/yy | 00/00/00 | ||||||
| -seqtype | list | Sequence type | 
 | unknown | ||||||
| -blastversion | list | Blast index version | 
 | unknown | ||||||
| -outfile | outfile | General log output file | Output file | <*>.dbiblast | ||||||
| Additional (Optional) qualifiers | ||||||||||
| (none) | ||||||||||
| Advanced (Unprompted) qualifiers | ||||||||||
| -fields | list | Index fields | 
 | acc | ||||||
| -exclude | string | Wildcard filename(s) to exclude | Any string | |||||||
| -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 | Any string | -T . -k 1,1 | ||||||
| -maxindex | integer | Maximum index length | Integer 0 or more | 0 | ||||||
| -[no]systemsort | boolean | Use system sort utility | Boolean value Yes/No | Yes | ||||||
| -[no]cleanup | boolean | Clean up temporary files | Boolean value Yes/No | Yes | ||||||
| -sourcefile | boolean | Use FASTA source file | Boolean value Yes/No | No | ||||||
| -indexoutdir | outdir | Index file output directory | Output directory | . | ||||||
| Associated qualifiers | ||||||||||
| "-directory" associated directory qualifiers | ||||||||||
| -extension | string | Default file extension | Any string | |||||||
| "-outfile" associated outfile qualifiers | ||||||||||
| -odirectory | string | Output directory | Any string | |||||||
| "-indexoutdir" associated outdir qualifiers | ||||||||||
| -extension | string | Default file extension | Any string | |||||||
| General qualifiers | ||||||||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N | ||||||
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N | ||||||
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N | ||||||
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N | ||||||
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N | ||||||
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y | ||||||
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N | ||||||
| -warning | boolean | Report warnings | Boolean value Yes/No | Y | ||||||
| -error | boolean | Report errors | Boolean value Yes/No | Y | ||||||
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y | ||||||
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y | ||||||
| -version | boolean | Report version number and exit | Boolean value Yes/No | N | ||||||
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| 
########################################
# Program: dbiblast
# Rundate: Mon 15 Jul 2013 12:00:00
# Dbname: swnew
# Release: 0.0
# Date: 15/07/13
# CurrentDirectory: /homes/user/test/qa/dbiblast-ex-keep/
# IndexDirectory: ./
# IndexDirectoryPath: /homes/user/test/qa/dbiblast-ex-keep/
# Maxindex: 0
# Fields: 2
#   Field 1: id
#   Field 2: acc
# Directory: /homes/user/test/data/
# DirectoryPath: /homes/user/test/data/
# Filenames: swnew
# Exclude: 
# Files: 1
#   File 1: /homes/user/test/data/swnew
########################################
# Commandline: dbiblast
#    -dbname swnew
#    -directory ../../data
########################################
filename: '/homes/user/test/data/swnew'
    id: 9
   acc: 9
Index acc: maxlen 6 items 9
Total 1 files 9 entries (0 duplicates)
 | 
dbiblast creates four index files. All are binary but with a simple format.
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 ]
The reason is that NCBI have not documented the new format, so we cannot extend dbiblast to read it.
If you have the original (fasta format) file you can build the previous blast database format with:
formatdb -A F
This turns off the new "ASN.1" formatting. blastall will still work.
| Program name | Description | 
|---|---|
| dbifasta | Index a fasta file database | 
| dbiflat | Index a flat file database | 
| dbigcg | Index a GCG formatted database | 
| dbxcompress | Compress an uncompressed dbx index | 
| dbxedam | Index the EDAM ontology using b+tree indices | 
| dbxfasta | Index a fasta file database using b+tree indices | 
| dbxflat | Index a flat file database using b+tree indices | 
| dbxgcg | Index a GCG formatted database using b+tree indices | 
| dbxobo | Index an obo ontology using b+tree indices | 
| dbxreport | Validate index and report internals for dbx databases | 
| dbxresource | Index a data resource catalogue using b+tree indices | 
| dbxstat | Dump statistics for dbx databases | 
| dbxtax | Index NCBI taxonomy using b+tree indices | 
| dbxuncompress | Uncompress a compressed dbx index | 
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.