
                              EMBOSS: dbiblast
     _________________________________________________________________
   
                               Program 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.
   
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     bool       Use system sort utility
   -[no]cleanup        bool       Clean up temporary files
   -sourcefile         bool       Use FASTA source file

   General qualifiers:
  -help                bool       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 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.
   
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@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
