|   | 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 ]
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.
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
| 
   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 is accepted)
   -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
                                  is accepted)
   -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 is accepted)
   -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:
   "-outfile" associated qualifiers
   -odirectory         string     Output directory
   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write 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. 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
 | 
| Standard (Mandatory) qualifiers | Allowed values | Default | |||||||
|---|---|---|---|---|---|---|---|---|---|
| [-dbname] (Parameter 1) | Database name | Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/ | Required | ||||||
| -directory | Database directory | Directory | . | ||||||
| -filenames | Wildcard database filename | Any string is accepted | Database name | ||||||
| -release | Release number | Any 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 | ||||||
| -outfile | General log output file | Output file | <*>.dbiblast | ||||||
| Additional (Optional) qualifiers | Allowed values | Default | |||||||
| (none) | |||||||||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |||||||
| -fields | Index fields | 
 | acc | ||||||
| -exclude | Wildcard filename(s) to exclude | Any string is accepted | An empty 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 | ||||||
| -indexoutdir | Index file output directory | Output directory | . | ||||||
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| 
########################################
# Program: dbiblast
# Rundate: Sun 15 Jul 2007 12:00:00
# Dbname: swnew
# Release: 0.0
# Date: 15/07/07
# 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.
| Program name | Description | 
|---|---|
| dbifasta | Database indexing for fasta file databases | 
| dbiflat | Index a flat file database | 
| dbigcg | Index a GCG formatted database | 
| dbxfasta | Database b+tree indexing for fasta file databases | 
| dbxflat | Database b+tree indexing for flat file databases | 
| dbxgcg | Database b+tree indexing for GCG formatted databases |