dbiblast

 

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Function

Index a BLAST database

Description

dbiblast indexes a blast database created by the NCBI indexing programs formatdb, pressdb or setdb, and builds EMBL CD-ROM format index files. This 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.

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.

Usage

Here is a sample session with dbiblast

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

Command line arguments

   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 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. 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
N (nucleic)
P (protein)
? (unknown)
unknown
-blastversion Blast index version
1 (wublast and setdb/pressdb)
2 (formatdb)
0 (unknown)
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 (acnum accession number index)
sv (seqvn sequence version and gi number index)
des (des description index)
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 .

Input file format

Any BLAST1 or BLAST2 database index files.

Output file format

Output files for usage example

File: division.lkp

This file contains non-printing characters and so cannot be displayed here.

File: entrynam.idx

This file contains non-printing characters and so cannot be displayed here.

File: acnum.hit

This file contains non-printing characters and so cannot be displayed here.

File: acnum.trg

This file contains non-printing characters and so cannot be displayed here.

File: outfile.dbiblast

########################################
# Program: dbiblast
# Rundate: Tue 15 Jul 2008 12:00:00
# Dbname: swnew
# Release: 0.0
# Date: 15/07/08
# 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.

Data files

None.

Notes

dbiblast can't use the new style of Blast indices. You must create the old style of Blast indices by adding -A F to the formatdb command line.

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
]  

Fields Indexed

By default, dbiblast will index the ID name and the accession number (if present).
If they are present in your database, you may specify that dbiblast should index the Sequence Version and GI number and the words in the description by using the '-fields' qualifier with the appropriate values.

Indexing the Blast database

dbiblast can't use the new style of Blast indices. You must create the old style of Blast indices by adding -A F to the formatdb command line.

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.

References

None.

Warnings

Diagnostic Error Messages

None.

Exit status

None.

Known bugs

dbiblast can't use the new style of Blast indices. You must create the old style of Blast indices by adding -A F to the formatdb command line.

See also

Program name Description
dbifasta Index a fasta file database
dbiflat Index a flat file database
dbigcg Index a GCG formatted database
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

Author(s)

Peter Rice (pmr © ebi.ac.uk)
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

History

Completed December 1999

Target users

This program is intended to be used by administrators responsible for software and database installation and maintenance.

Comments

None