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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, using a blast 2 protein database.
% dbiblast
NCBI : NCBI with | characters
GCG : GCG format dbname:entryname
SIMPLE : ID and accession
ID : entryname
UNKNOWN : unknown
Entry format [unknown]: gcg
Database name: swnew
Database directory [.]: /nfs/disk42/pmr/emboss/test/blastp2/
database base filename [swnew]:
Release number [0.0]:
Index date [00/00/00]: 04/02/00
N : nucleic
P : protein
? : unknown
Sequence type [unknown]: p
1 : wublast and setdb/pressdb
2 : formatdb
0 : unknown
Blast index version [unknown]: 2
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
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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) |
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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 |
Yes/No |
Yes |
-[no]cleanup |
Clean up temporary files |
Yes/No |
Yes |
-sourcefile |
Use FASTA source file |
Yes/No |
No |
Input file format
An NCBI BLAST1 or BLAST2 database.
Output file format
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
None.
Diagnostic Error Messages
None.
Exit status
None.
Known bugs
None.
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@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