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
]  

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

   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
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.

Data files

None.

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

None.

Known bugs

None.

See also

Program nameDescription
dbifastaIndex a fasta database
dbiflatIndex a flat file database
dbigcgIndex a GCG formatted database

Author(s)

This application was written by Peter Rice (pmr@sanger.ac.uk) Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, 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