| dbiblast

## 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.

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.

## 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]:

Go to the output files for this example

## Command line arguments

       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

       Associated qualifiers: (none)
       General qualifiers:
       -auto                boolean    Turn off prompts
       -stdout              boolean    Write standard output
       -filter              boolean    Read standard input, write standard output
       -options             boolean    Prompt for required and optional values
       -debug               boolean    Write debug output to program.dbg
       -acdlog              boolean    Write ACD processing log to program.acdlog
       -acdpretty           boolean    Rewrite ACD file as program.acdpretty
       -acdtable            boolean    Write HTML table of options
       -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 deaths

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 |
N | (nucleic)
P | (protein)
? | (unknown)
| unknown
-blastversion | Blast index version |
1 | (wublast and setdb/pressdb)
2 | (formatdb)
0 | (unknown)
| unknown
Optional qualifiers | Allowed values | Default
(none)
Advanced qualifiers | Allowed values | Default
-fields | Index fields |
acnum | (Accession number)
seqvn | (Sequence Version and GI)
des | (Description)
| 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

## Input file format

AI BLAST1 or BLAST2 database index files.

## Output file format

### Output files for usage example

### 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: 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.

dbiblast creates four index files. All are binary but with a simple format.

- division.lkp is the master index file, and has a 300 byte header containing the database name and date plus information on the record size. This header is followed by one record for each database file, giving the full file name for the data file, and optionally a second sequence file.

- entryname.idx is the entry name index. It has the same 300 byte header, mainly used to store the record size which will depend on the size of the longest entryname in the database. Each entry is stored in sorted alphanumeric order so that a binary search can be used to efficiently find any record. The record also holds the file number from division.lkp and the offsets in the data and sequence files for that entry.
- acnum.trg holds the accession number information. The file has the usual 300 byte header, and a sorted list of record by accession number. Each accession number record contains the first record number in acnum.hit and the total number of records in acnum.hit so that secondary (duplicated) accession numbers can be searched.
- acnum.hit is a very simple file. After the usual 300 byte header, each record simply holds the record number in entryname.idx. An accession number search will use acnum.trg to find a start position and number of records to read in this file, and will then simply read the entryname.idx records for each entry in turn.

## Data files

None.

## Notes

None.

## References

None.

## Warnings

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.

## 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 database
dbiflat | Index a flat file database
dbigcg | Index a GCG formatted database

## Author(s)

This application was written by Peter Rice (pmr © ebi.ac.uk)
Informatics Division, 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