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<HTML>

<HEAD>
  <TITLE>
  EMBOSS: dbiblast
  </TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">

<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="/images/emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
dbiblast
</font></b>
</td></tr>
</table>
<br>&nbsp;
<p>


<H2>
Wiki
</H2>

The master copies of EMBOSS documentation are available
at <a href="http://emboss.open-bio.org/wiki/Appdocs">
http://emboss.open-bio.org/wiki/Appdocs</a>
on the EMBOSS Wiki.

<p>
Please help by correcting and extending the Wiki pages.

<H2>
    Function
</H2>
Index a BLAST database
<H2>
    Description
</H2>

<b>dbiblast</b> 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.

<p>

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.

<p>

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, <b>dbiblast</b> will ask about the database
type. If the answer is "unknown" <b>dbiblast</b> will test each possible set
of file names until one is found.



<H2>
    Usage
</H2>
Here is a sample session with <b>dbiblast</b>
<p>
This creates EMBOSS indices for the BLAST database 'swnew' 
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>dbiblast </b>
Index a BLAST database
Database name: <b>swnew</b>
Database directory [.]: <b>data</b>
Wildcard database filename [swnew]: <b></b>
Release number [0.0]: <b></b>
Index date [00/00/00]: <b></b>
         N : nucleic
         P : protein
         ? : unknown
Sequence type [unknown]: <b></b>
         1 : wublast and setdb/pressdb
         2 : formatdb
         0 : unknown
Blast index version [unknown]: <b></b>
General log output file [outfile.dbiblast]: <b></b>

</pre></td></tr></table><p>
<p>
<a href="#output.1">Go to the output files for this example</a><p><p>


<H2>
    Command line arguments
</H2>

<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
Index a BLAST database
Version: EMBOSS:6.6.0.0

   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)
   -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)
   -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)
   -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:

   "-directory" associated qualifiers
   -extension          string     Default file extension

   "-outfile" associated qualifiers
   -odirectory         string     Output directory

   "-indexoutdir" associated qualifiers
   -extension          string     Default file extension

   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 and exit. 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
   -version            boolean    Report version number and exit

</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left">Qualifier</th>
<th align="left">Type</th>
<th align="left">Description</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-dbname]<br>(Parameter 1)</td>
<td>string</td>
<td>Database name</td>
<td>Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/</td>
<td><b>Required</b></td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-directory</td>
<td>directory</td>
<td>Database directory</td>
<td>Directory</td>
<td>.</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-filenames</td>
<td>string</td>
<td>Wildcard database filename</td>
<td>Any string</td>
<td>Database name</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-release</td>
<td>string</td>
<td>Release number</td>
<td>Any string up to 9 characters</td>
<td>0.0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-date</td>
<td>string</td>
<td>Index date</td>
<td>Date string dd/mm/yy</td>
<td>00/00/00</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-seqtype</td>
<td>list</td>
<td>Sequence type</td>
<td><table><tr><td>N</td> <td><i>(nucleic)</i></td></tr><tr><td>P</td> <td><i>(protein)</i></td></tr><tr><td>?</td> <td><i>(unknown)</i></td></tr></table></td>
<td>unknown</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-blastversion</td>
<td>list</td>
<td>Blast index version</td>
<td><table><tr><td>1</td> <td><i>(wublast and setdb/pressdb)</i></td></tr><tr><td>2</td> <td><i>(formatdb)</i></td></tr><tr><td>0</td> <td><i>(unknown)</i></td></tr></table></td>
<td>unknown</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-outfile</td>
<td>outfile</td>
<td>General log output file</td>
<td>Output file</td>
<td><i>&lt;*&gt;</i>.dbiblast</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Additional (Optional) qualifiers</th>
</tr>

<tr>
<td colspan=5>(none)</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>-fields</td>
<td>list</td>
<td>Index fields</td>
<td><table><tr><td>acc</td> <td><i>(acnum accession number index)</i></td></tr><tr><td>sv</td> <td><i>(seqvn sequence version and gi number index)</i></td></tr><tr><td>des</td> <td><i>(des description index)</i></td></tr></table></td>
<td>acc</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-exclude</td>
<td>string</td>
<td>Wildcard filename(s) to exclude</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-sortoptions</td>
<td>string</td>
<td>Sort options, typically '-T .' to use current directory for work files and '-k 1,1' to force GNU sort to use the first field</td>
<td>Any string</td>
<td>-T . -k 1,1</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-maxindex</td>
<td>integer</td>
<td>Maximum index length</td>
<td>Integer 0 or more</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-[no]systemsort</td>
<td>boolean</td>
<td>Use system sort utility</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-[no]cleanup</td>
<td>boolean</td>
<td>Clean up temporary files</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-sourcefile</td>
<td>boolean</td>
<td>Use FASTA source file</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-indexoutdir</td>
<td>outdir</td>
<td>Index file output directory</td>
<td>Output directory</td>
<td>.</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Associated qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-directory" associated directory qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -extension</td>
<td>string</td>
<td>Default file extension</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-outfile" associated outfile qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -odirectory</td>
<td>string</td>
<td>Output directory</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-indexoutdir" associated outdir qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -extension</td>
<td>string</td>
<td>Default file extension</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>General qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td> -auto</td>
<td>boolean</td>
<td>Turn off prompts</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -stdout</td>
<td>boolean</td>
<td>Write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -filter</td>
<td>boolean</td>
<td>Read first file from standard input, write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -options</td>
<td>boolean</td>
<td>Prompt for standard and additional values</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -debug</td>
<td>boolean</td>
<td>Write debug output to program.dbg</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -verbose</td>
<td>boolean</td>
<td>Report some/full command line options</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -help</td>
<td>boolean</td>
<td>Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -warning</td>
<td>boolean</td>
<td>Report warnings</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -error</td>
<td>boolean</td>
<td>Report errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fatal</td>
<td>boolean</td>
<td>Report fatal errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -die</td>
<td>boolean</td>
<td>Report dying program messages</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -version</td>
<td>boolean</td>
<td>Report version number and exit</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

</table>

<H2>
    Input file format
</H2>

Any BLAST1 or BLAST2 database index files.

<p>

<H2>
    Output file format
</H2>


<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: division.lkp</h3>
<p>This file contains non-printing characters and so cannot be displayed here.
<p><h3>File: entrynam.idx</h3>
<p>This file contains non-printing characters and so cannot be displayed here.
<p><h3>File: acnum.hit</h3>
<p>This file contains non-printing characters and so cannot be displayed here.
<p><h3>File: acnum.trg</h3>
<p>This file contains non-printing characters and so cannot be displayed here.
<p><h3>File: outfile.dbiblast</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
########################################
# Program: dbiblast
# Rundate: Mon 15 Jul 2013 12:00:00
# Dbname: swnew
# Release: 0.0
# Date: 15/07/13
# 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)
</pre>
</td></tr></table><p>
<p>

<b>dbiblast</b> creates four index files.  All are binary but with a
simple format. 

<ul>

<li>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.

<p>

<li>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.

<li>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.

<li>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.

</ul>

<H2>
    Data files
</H2>


None.

<H2>
    Notes
</H2>

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


<p>

Having created the EMBOSS indices for this file, a database can then be
defined in the file <b>emboss.defaults</b> as something like:

<p>

<pre>
DB swnew [
   type: P
   format: embl
   method: blast
   directory: /data/embl
]  
</pre>


<h3>Fields Indexed</H3>

By default, <b>dbiblast</b> will index the ID name and the accession number (if present).

<br>

If they are present in your database, you may specify that
<b>dbiblast</b> should index the Sequence Version and GI number and the
words in the description by using the '-fields' qualifier with the
appropriate values. 

<h3>Indexing the Blast database</h3>

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

<p>

The reason is that NCBI have not documented the new format, so we cannot
extend dbiblast to read it.

<p>

If you have the original (fasta format) file you can build the previous
blast database format with:

<p>

<i>formatdb -A F</i>

<p>

This turns off the new "ASN.1" formatting. blastall will still work. 


<H2>
    References
</H2>

None.


<H2>
    Warnings
</H2>


<H2>
    Diagnostic Error Messages
</H2>

None.


<H2>
    Exit status
</H2>

None.


<H2>
    Known bugs
</H2>

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

<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th>
<th>Description</th></tr>
<tr>
<td><a href="dbifasta.html">dbifasta</a></td>
<td>Index a fasta file database</td>
</tr>

<tr>
<td><a href="dbiflat.html">dbiflat</a></td>
<td>Index a flat file database</td>
</tr>

<tr>
<td><a href="dbigcg.html">dbigcg</a></td>
<td>Index a GCG formatted database</td>
</tr>

<tr>
<td><a href="dbxcompress.html">dbxcompress</a></td>
<td>Compress an uncompressed dbx index</td>
</tr>

<tr>
<td><a href="dbxedam.html">dbxedam</a></td>
<td>Index the EDAM ontology using b+tree indices</td>
</tr>

<tr>
<td><a href="dbxfasta.html">dbxfasta</a></td>
<td>Index a fasta file database using b+tree indices</td>
</tr>

<tr>
<td><a href="dbxflat.html">dbxflat</a></td>
<td>Index a flat file database using b+tree indices</td>
</tr>

<tr>
<td><a href="dbxgcg.html">dbxgcg</a></td>
<td>Index a GCG formatted database using b+tree indices</td>
</tr>

<tr>
<td><a href="dbxobo.html">dbxobo</a></td>
<td>Index an obo ontology using b+tree indices</td>
</tr>

<tr>
<td><a href="dbxreport.html">dbxreport</a></td>
<td>Validate index and report internals for dbx databases</td>
</tr>

<tr>
<td><a href="dbxresource.html">dbxresource</a></td>
<td>Index a data resource catalogue using b+tree indices</td>
</tr>

<tr>
<td><a href="dbxstat.html">dbxstat</a></td>
<td>Dump statistics for dbx databases</td>
</tr>

<tr>
<td><a href="dbxtax.html">dbxtax</a></td>
<td>Index NCBI taxonomy using b+tree indices</td>
</tr>

<tr>
<td><a href="dbxuncompress.html">dbxuncompress</a></td>
<td>Uncompress a compressed dbx index</td>
</tr>

</table>
<H2>
    Author(s)
</H2>

Peter Rice
<br>
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.
<H2>
    History
</H2>

Completed December 1999

<H2>
    Target users
</H2>
This program is intended to be used by administrators responsible
for software and database installation and maintenance. 

<H2>
    Comments
</H2>
None



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