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<HTML>

<HEAD>
  <TITLE>
  EMBOSS: showdb
  </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="emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
showdb
</font></b>
</td></tr>
</table>
<br>&nbsp;
<p>


<H2>
    Function
</H2>
Displays information on the currently available databases

<H2>
    Description
</H2>


This writes out a simple table displaying the names, contents and
available ways of accessing the sequence databases.

<p>
The available ways of accessing the databases are 'ID', 'Query' and
'All'.  These refer to the way that you can search the databases to
get entries from them, which is governed by the ways the database has
been set up and the way it is organised and indexed.

<p>
Different databases may have different access capabilities, depending
on how your local site is organised.

<p>
EMBOSS has been designed to be extremely flexible in its use of
sequence databases formats, so that it is easy to set EMBOSS up to use
your site's existing databases.  Sometimes this means that it is hard
to extract entries from some databases in particular ways.  For
example, a flat file database with no index is only useful for reading
all entries, while a database located in another site that is
available via the WWW may only provide single entries.

<p>
'ID' (also known as 'single entry') allows the programs to extract a
single explicitly named entry from the database, for example
embl:x13776

<p>
'Query' (also known as 'wild') indicates that programs can extract a
set of matching wildcard entry names (this may be slow for some
methods of access).  For example you can look at all of the human PAX
proteins in SWISS_PROT by: swissprot:pax*_human

<p>
'All' allows the programs to analyse all the entries in the database
sequentially.  For example this lets you look at all entries in the
database with the notation: embl:*

<p>
A database may have several different methods of access available.
Ideally all of the databases available on your site will be available
in all three ways, but this is not the best of all posssible worlds
and so you might like to check how you can access the databases by
running this program and having a look.

<H2>
    Usage
</H2>
<b>Here is a sample session with showdb</b>
<p>
Display information on the currently available databases: 
<p>

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

% <b>showdb </b>
Displays information on the currently available databases

# Name           Type  ID  Qry All Comment
# ============== ==== ==  === === =======
qapblast         P    OK  OK  OK  BLAST swissnew
qapblastall      P    OK  OK  OK  BLAST swissnew, all fields indexed
qapblastsplit    P    OK  OK  OK  BLAST swissnew split in 5 files
qapblastsplitexc P    OK  OK  OK  BLAST swissnew split in 5 files, not file 02
qapblastsplitinc P    OK  OK  OK  BLAST swissnew split in 5 files, only file 02
qapfasta         P    OK  OK  OK  FASTA file swissnew entries
qapflat          P    OK  OK  OK  SpTrEmbl flatfile
qapflatall       P    OK  OK  OK  SpTrEmbl flatfiles, all fields indexed
qapir            P    OK  OK  OK  PIR
qapirall         P    OK  OK  OK  PIR
qapirinc         P    OK  OK  OK  PIR
qapxfasta        P    OK  OK  OK  FASTA file swissnew entries
qapxflat         P    OK  OK  OK  Swissnew flatfiles
qaxpir           P    OK  OK  OK  PIR
qaxpirall        P    OK  OK  OK  PIR
qaxpirinc        P    OK  OK  OK  PIR
tpir             P    OK  OK  OK  PIR using NBRF access for 4 files
tsw              P    OK  OK  OK  Swissprot native format with EMBL CD-ROM index
tswnew           P    OK  OK  OK  SpTrEmbl as 3 files in native format with EMBL CD-ROM index
twp              P    OK  OK  OK  EMBL new in native format with EMBL CD-ROM index
genbanksrs       N    OK  -   -   Genbank IDs
qanfasta         N    OK  OK  OK  FASTA file EMBL rodents
qanfastaall      N    OK  OK  OK  FASTA file EMBL rodents, all fields indexed
qanflat          N    OK  OK  OK  EMBL flatfiles
qanflatall       N    OK  OK  OK  EMBL flatfiles
qanflatexc       N    OK  OK  OK  EMBL flatfiles, no rodent file
qanflatinc       N    OK  OK  OK  EMBL flatfiles, only rodent file
qangcg           N    OK  OK  OK  GCG format EMBL
qangcgall        N    OK  OK  OK  GCG format EMBL
qangcgexc        N    OK  OK  OK  GCG format EMBL without prokaryotes
qangcginc        N    OK  OK  OK  GCG format EMBL only prokaryotes
qanxfasta        N    OK  OK  OK  FASTA file EMBL rodents
qanxfastaall     N    OK  OK  OK  FASTA file EMBL rodents, all fields indexed
qanxflat         N    OK  OK  OK  EMBL flatfiles
qanxflatall      N    OK  OK  OK  EMBL flatfiles, all fields indexed
qanxflatexc      N    OK  OK  OK  EMBL flatfiles, no rodent file
qanxflatinc      N    OK  OK  OK  EMBL flatfiles, only rodent file
qanxgcg          N    OK  OK  OK  GCG format EMBL
qanxgcgall       N    OK  OK  OK  GCG format EMBL
qanxgcgexc       N    OK  OK  OK  GCG format EMBL without prokaryotes
qanxgcginc       N    OK  OK  OK  GCG format EMBL only prokaryotes
qapirexc         N    OK  OK  OK  PIR
qasrswww         N    OK  -   -   Remote SRS web server
qawfasta         N    OK  OK  OK  FASTA file wormpep entries
qawxfasta        N    OK  OK  OK  FASTA file wormpep entries
qaxpirexc        N    OK  OK  OK  PIR
tembl            N    OK  OK  OK  EMBL in native format with EMBL CD-ROM index
temblall         N    -   -   OK  EMBL in native format with EMBL CD-ROM index
temblrest        N    -   -   OK  EMBL in native format with EMBL CD-ROM index
temblvrt         N    -   -   OK  EMBL in native format with EMBL CD-ROM index
testdb           N    OK  OK  OK  test sequence data
tgb              N    OK  -   -   Genbank IDs
tgenbank         N    OK  OK  OK  GenBank in native format with EMBL CD-ROM index

</pre></td></tr></table><p>
<p>
<p>
<p>
<b>Example 2</b>
<p>
Write the results to a file: 
<p>

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

% <b>showdb -outfile showdb.out </b>
Displays information on the currently available databases

</pre></td></tr></table><p>
<p>
<a href="#output.2">Go to the output files for this example</a><p><p>
<p>
<b>Example 3</b>
<p>
Display information on one explicit database: 
<p>

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

% <b>showdb -database tsw </b>
Displays information on the currently available databases

# Name         Type  ID  Qry All Comment
# ============ ==== ==  === === =======
tsw            P    OK  OK  OK  Swissprot native format with EMBL CD-ROM index

</pre></td></tr></table><p>
<p>
<a href="#input.3">Go to the input files for this example</a><br><p>
<p>
<b>Example 4</b>
<p>
Display information on the databases formatted in HTML: 
<p>

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

% <b>showdb -html </b>
Displays information on the currently available databases

<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Name</th><th>Type</th><th>ID</th><th>Qry</th><th>All</th><th>Comment</th></tr>
<tr><td>qapblast</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>BLAST swissnew</td></tr>
<tr><td>qapblastall</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>BLAST swissnew, all fields indexed</td></tr>
<tr><td>qapblastsplit</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>BLAST swissnew split in 5 files</td></tr>
<tr><td>qapblastsplitexc</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>BLAST swissnew split in 5 files, not file 02</td></tr>
<tr><td>qapblastsplitinc</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>BLAST swissnew split in 5 files, only file 02</td></tr>
<tr><td>qapfasta</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>FASTA file swissnew entries</td></tr>
<tr><td>qapflat</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>SpTrEmbl flatfile</td></tr>
<tr><td>qapflatall</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>SpTrEmbl flatfiles, all fields indexed</td></tr>
<tr><td>qapir</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>PIR</td></tr>
<tr><td>qapirall</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>PIR</td></tr>
<tr><td>qapirinc</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>PIR</td></tr>
<tr><td>qapxfasta</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>FASTA file swissnew entries</td></tr>
<tr><td>qapxflat</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>Swissnew flatfiles</td></tr>
<tr><td>qaxpir</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>PIR</td></tr>
<tr><td>qaxpirall</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>PIR</td></tr>
<tr><td>qaxpirinc</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>PIR</td></tr>
<tr><td>tpir</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>PIR using NBRF access for 4 files</td></tr>
<tr><td>tsw</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>Swissprot native format with EMBL CD-ROM index</td></tr>
<tr><td>tswnew</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>SpTrEmbl as 3 files in native format with EMBL CD-ROM index</td></tr>
<tr><td>twp</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>EMBL new in native format with EMBL CD-ROM index</td></tr>
<tr><td>genbanksrs</td><td>N</td><td>OK  </td><td>-   </td><td>-   </td><td>Genbank IDs</td></tr>
<tr><td>qanfasta</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>FASTA file EMBL rodents</td></tr>
<tr><td>qanfastaall</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>FASTA file EMBL rodents, all fields indexed</td></tr>
<tr><td>qanflat</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>EMBL flatfiles</td></tr>
<tr><td>qanflatall</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>EMBL flatfiles</td></tr>
<tr><td>qanflatexc</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>EMBL flatfiles, no rodent file</td></tr>
<tr><td>qanflatinc</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>EMBL flatfiles, only rodent file</td></tr>
<tr><td>qangcg</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>GCG format EMBL</td></tr>
<tr><td>qangcgall</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>GCG format EMBL</td></tr>
<tr><td>qangcgexc</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>GCG format EMBL without prokaryotes</td></tr>
<tr><td>qangcginc</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>GCG format EMBL only prokaryotes</td></tr>
<tr><td>qanxfasta</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>FASTA file EMBL rodents</td></tr>
<tr><td>qanxfastaall</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>FASTA file EMBL rodents, all fields indexed</td></tr>
<tr><td>qanxflat</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>EMBL flatfiles</td></tr>
<tr><td>qanxflatall</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>EMBL flatfiles, all fields indexed</td></tr>
<tr><td>qanxflatexc</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>EMBL flatfiles, no rodent file</td></tr>
<tr><td>qanxflatinc</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>EMBL flatfiles, only rodent file</td></tr>
<tr><td>qanxgcg</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>GCG format EMBL</td></tr>
<tr><td>qanxgcgall</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>GCG format EMBL</td></tr>
<tr><td>qanxgcgexc</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>GCG format EMBL without prokaryotes</td></tr>
<tr><td>qanxgcginc</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>GCG format EMBL only prokaryotes</td></tr>
<tr><td>qapirexc</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>PIR</td></tr>
<tr><td>qasrswww</td><td>N</td><td>OK  </td><td>-   </td><td>-   </td><td>Remote SRS web server</td></tr>
<tr><td>qawfasta</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>FASTA file wormpep entries</td></tr>
<tr><td>qawxfasta</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>FASTA file wormpep entries</td></tr>
<tr><td>qaxpirexc</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>PIR</td></tr>
<tr><td>tembl</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>EMBL in native format with EMBL CD-ROM index</td></tr>
<tr><td>temblall</td><td>N</td><td>-   </td><td>-   </td><td>OK  </td><td>EMBL in native format with EMBL CD-ROM index</td></tr>
<tr><td>temblrest</td><td>N</td><td>-   </td><td>-   </td><td>OK  </td><td>EMBL in native format with EMBL CD-ROM index</td></tr>
<tr><td>temblvrt</td><td>N</td><td>-   </td><td>-   </td><td>OK  </td><td>EMBL in native format with EMBL CD-ROM index</td></tr>
<tr><td>testdb</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>test sequence data</td></tr>
<tr><td>tgb</td><td>N</td><td>OK  </td><td>-   </td><td>-   </td><td>Genbank IDs</td></tr>
<tr><td>tgenbank</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>GenBank in native format with EMBL CD-ROM index</td></tr>
</table>

</pre></td></tr></table><p>
<p>
<p>
<p>
<b>Example 5</b>
<p>
Display protein databases only: 
<p>

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

% <b>showdb -nonucleic </b>
Displays information on the currently available databases

# Name           Type  ID  Qry All Comment
# ============== ==== ==  === === =======
qapblast         P    OK  OK  OK  BLAST swissnew
qapblastall      P    OK  OK  OK  BLAST swissnew, all fields indexed
qapblastsplit    P    OK  OK  OK  BLAST swissnew split in 5 files
qapblastsplitexc P    OK  OK  OK  BLAST swissnew split in 5 files, not file 02
qapblastsplitinc P    OK  OK  OK  BLAST swissnew split in 5 files, only file 02
qapfasta         P    OK  OK  OK  FASTA file swissnew entries
qapflat          P    OK  OK  OK  SpTrEmbl flatfile
qapflatall       P    OK  OK  OK  SpTrEmbl flatfiles, all fields indexed
qapir            P    OK  OK  OK  PIR
qapirall         P    OK  OK  OK  PIR
qapirinc         P    OK  OK  OK  PIR
qapxfasta        P    OK  OK  OK  FASTA file swissnew entries
qapxflat         P    OK  OK  OK  Swissnew flatfiles
qaxpir           P    OK  OK  OK  PIR
qaxpirall        P    OK  OK  OK  PIR
qaxpirinc        P    OK  OK  OK  PIR
tpir             P    OK  OK  OK  PIR using NBRF access for 4 files
tsw              P    OK  OK  OK  Swissprot native format with EMBL CD-ROM index
tswnew           P    OK  OK  OK  SpTrEmbl as 3 files in native format with EMBL CD-ROM index
twp              P    OK  OK  OK  EMBL new in native format with EMBL CD-ROM index

</pre></td></tr></table><p>
<p>
<p>
<p>
<b>Example 6</b>
<p>
Display the information with no headings: 
<p>

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

% <b>showdb -noheading </b>
Displays information on the currently available databases

qapblast         P    OK  OK  OK  BLAST swissnew
qapblastall      P    OK  OK  OK  BLAST swissnew, all fields indexed
qapblastsplit    P    OK  OK  OK  BLAST swissnew split in 5 files
qapblastsplitexc P    OK  OK  OK  BLAST swissnew split in 5 files, not file 02
qapblastsplitinc P    OK  OK  OK  BLAST swissnew split in 5 files, only file 02
qapfasta         P    OK  OK  OK  FASTA file swissnew entries
qapflat          P    OK  OK  OK  SpTrEmbl flatfile
qapflatall       P    OK  OK  OK  SpTrEmbl flatfiles, all fields indexed
qapir            P    OK  OK  OK  PIR
qapirall         P    OK  OK  OK  PIR
qapirinc         P    OK  OK  OK  PIR
qapxfasta        P    OK  OK  OK  FASTA file swissnew entries
qapxflat         P    OK  OK  OK  Swissnew flatfiles
qaxpir           P    OK  OK  OK  PIR
qaxpirall        P    OK  OK  OK  PIR
qaxpirinc        P    OK  OK  OK  PIR
tpir             P    OK  OK  OK  PIR using NBRF access for 4 files
tsw              P    OK  OK  OK  Swissprot native format with EMBL CD-ROM index
tswnew           P    OK  OK  OK  SpTrEmbl as 3 files in native format with EMBL CD-ROM index
twp              P    OK  OK  OK  EMBL new in native format with EMBL CD-ROM index
genbanksrs       N    OK  -   -   Genbank IDs
qanfasta         N    OK  OK  OK  FASTA file EMBL rodents
qanfastaall      N    OK  OK  OK  FASTA file EMBL rodents, all fields indexed
qanflat          N    OK  OK  OK  EMBL flatfiles
qanflatall       N    OK  OK  OK  EMBL flatfiles
qanflatexc       N    OK  OK  OK  EMBL flatfiles, no rodent file
qanflatinc       N    OK  OK  OK  EMBL flatfiles, only rodent file
qangcg           N    OK  OK  OK  GCG format EMBL
qangcgall        N    OK  OK  OK  GCG format EMBL
qangcgexc        N    OK  OK  OK  GCG format EMBL without prokaryotes
qangcginc        N    OK  OK  OK  GCG format EMBL only prokaryotes
qanxfasta        N    OK  OK  OK  FASTA file EMBL rodents
qanxfastaall     N    OK  OK  OK  FASTA file EMBL rodents, all fields indexed
qanxflat         N    OK  OK  OK  EMBL flatfiles
qanxflatall      N    OK  OK  OK  EMBL flatfiles, all fields indexed
qanxflatexc      N    OK  OK  OK  EMBL flatfiles, no rodent file
qanxflatinc      N    OK  OK  OK  EMBL flatfiles, only rodent file
qanxgcg          N    OK  OK  OK  GCG format EMBL
qanxgcgall       N    OK  OK  OK  GCG format EMBL
qanxgcgexc       N    OK  OK  OK  GCG format EMBL without prokaryotes
qanxgcginc       N    OK  OK  OK  GCG format EMBL only prokaryotes
qapirexc         N    OK  OK  OK  PIR
qasrswww         N    OK  -   -   Remote SRS web server
qawfasta         N    OK  OK  OK  FASTA file wormpep entries
qawxfasta        N    OK  OK  OK  FASTA file wormpep entries
qaxpirexc        N    OK  OK  OK  PIR
tembl            N    OK  OK  OK  EMBL in native format with EMBL CD-ROM index
temblall         N    -   -   OK  EMBL in native format with EMBL CD-ROM index
temblrest        N    -   -   OK  EMBL in native format with EMBL CD-ROM index
temblvrt         N    -   -   OK  EMBL in native format with EMBL CD-ROM index
testdb           N    OK  OK  OK  test sequence data
tgb              N    OK  -   -   Genbank IDs
tgenbank         N    OK  OK  OK  GenBank in native format with EMBL CD-ROM index

</pre></td></tr></table><p>
<p>
<p>
<p>
<b>Example 7</b>
<p>
Display just a list of the available database names: 
<p>

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

% <b>showdb -noheading -notype -noid -noquery -noall -nocomment -auto </b>

qapblast         
qapblastall      
qapblastsplit    
qapblastsplitexc 
qapblastsplitinc 
qapfasta         
qapflat          
qapflatall       
qapir            
qapirall         
qapirinc         
qapxfasta        
qapxflat         
qaxpir           
qaxpirall        
qaxpirinc        
tpir             
tsw              
tswnew           
twp              
genbanksrs       
qanfasta         
qanfastaall      
qanflat          
qanflatall       
qanflatexc       
qanflatinc       
qangcg           
qangcgall        
qangcgexc        
qangcginc        
qanxfasta        
qanxfastaall     
qanxflat         
qanxflatall      
qanxflatexc      
qanxflatinc      
qanxgcg          
qanxgcgall       
qanxgcgexc       
qanxgcginc       
qapirexc         
qasrswww         
qawfasta         
qawxfasta        
qaxpirexc        
tembl            
temblall         
temblrest        
temblvrt         
testdb           
tgb              
tgenbank         

</pre></td></tr></table><p>
<p>
<p>
<p>
<b>Example 8</b>
<p>
Display only the names and types: 
<p>

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

% <b>showdb -only -type </b>
Displays information on the currently available databases

qapblast         P    
qapblastall      P    
qapblastsplit    P    
qapblastsplitexc P    
qapblastsplitinc P    
qapfasta         P    
qapflat          P    
qapflatall       P    
qapir            P    
qapirall         P    
qapirinc         P    
qapxfasta        P    
qapxflat         P    
qaxpir           P    
qaxpirall        P    
qaxpirinc        P    
tpir             P    
tsw              P    
tswnew           P    
twp              P    
genbanksrs       N    
qanfasta         N    
qanfastaall      N    
qanflat          N    
qanflatall       N    
qanflatexc       N    
qanflatinc       N    
qangcg           N    
qangcgall        N    
qangcgexc        N    
qangcginc        N    
qanxfasta        N    
qanxfastaall     N    
qanxflat         N    
qanxflatall      N    
qanxflatexc      N    
qanxflatinc      N    
qanxgcg          N    
qanxgcgall       N    
qanxgcgexc       N    
qanxgcginc       N    
qapirexc         N    
qasrswww         N    
qawfasta         N    
qawxfasta        N    
qaxpirexc        N    
tembl            N    
temblall         N    
temblrest        N    
temblvrt         N    
testdb           N    
tgb              N    
tgenbank         N    

</pre></td></tr></table><p>
<p>
<p>
<p>
<b>Example 9</b>
<p>
Display everything 
<p>

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

% <b>showdb -full </b>
Displays information on the currently available databases

# Name           Type  ID  Qry All Method    Fields            Defined  Release  Comment
# ============== ==== ==  === === ========= ================= ======= ======= =======
qapblast         P    OK  OK  OK  blast     -                 special         BLAST swissnew
qapblastall      P    OK  OK  OK  blast     sv,des            special         BLAST swissnew, all fields indexed
qapblastsplit    P    OK  OK  OK  blast     -                 special         BLAST swissnew split in 5 files
qapblastsplitexc P    OK  OK  OK  blast     -                 special         BLAST swissnew split in 5 files, not file 02
qapblastsplitinc P    OK  OK  OK  blast     -                 special         BLAST swissnew split in 5 files, only file 02
qapfasta         P    OK  OK  OK  emblcd    -                 special         FASTA file swissnew entries
qapflat          P    OK  OK  OK  emblcd    -                 special         SpTrEmbl flatfile
qapflatall       P    OK  OK  OK  emblcd    sv,des,org,key    special         SpTrEmbl flatfiles, all fields indexed
qapir            P    OK  OK  OK  gcg       -                 special         PIR
qapirall         P    OK  OK  OK  gcg       des,org,key       special         PIR
qapirinc         P    OK  OK  OK  gcg       -                 special         PIR
qapxfasta        P    OK  OK  OK  emboss    -                 special         FASTA file swissnew entries
qapxflat         P    OK  OK  OK  emboss    -                 special         Swissnew flatfiles
qaxpir           P    OK  OK  OK  embossgcg -                 special         PIR
qaxpirall        P    OK  OK  OK  embossgcg des,org,key       special         PIR
qaxpirinc        P    OK  OK  OK  embossgcg -                 special         PIR
tpir             P    OK  OK  OK  gcg       des,org,key       special         PIR using NBRF access for 4 files
tsw              P    OK  OK  OK  emblcd    sv,des,org,key    special 36      Swissprot native format with EMBL CD-ROM index
tswnew           P    OK  OK  OK  emblcd    sv,des,org,key    special 37      SpTrEmbl as 3 files in native format with EMBL CD-ROM index
twp              P    OK  OK  OK  emblcd    des               special 16      EMBL new in native format with EMBL CD-ROM index
genbanksrs       N    OK  -   -   srswww    gi,sv,des,org,key global          Genbank IDs
qanfasta         N    OK  OK  OK  emblcd    -                 special         FASTA file EMBL rodents
qanfastaall      N    OK  OK  OK  emblcd    sv,des            special         FASTA file EMBL rodents, all fields indexed
qanflat          N    OK  OK  OK  emblcd    -                 special         EMBL flatfiles
qanflatall       N    OK  OK  OK  emblcd    -                 special         EMBL flatfiles
qanflatexc       N    OK  OK  OK  emblcd    -                 special         EMBL flatfiles, no rodent file
qanflatinc       N    OK  OK  OK  emblcd    -                 special         EMBL flatfiles, only rodent file
qangcg           N    OK  OK  OK  gcg       -                 special         GCG format EMBL
qangcgall        N    OK  OK  OK  gcg       sv,des,org,key    special         GCG format EMBL
qangcgexc        N    OK  OK  OK  gcg       -                 special         GCG format EMBL without prokaryotes
qangcginc        N    OK  OK  OK  gcg       -                 special         GCG format EMBL only prokaryotes
qanxfasta        N    OK  OK  OK  emboss    -                 special         FASTA file EMBL rodents
qanxfastaall     N    OK  OK  OK  emboss    sv,des            special         FASTA file EMBL rodents, all fields indexed
qanxflat         N    OK  OK  OK  emboss    -                 special         EMBL flatfiles
qanxflatall      N    OK  OK  OK  emboss    des,org,key       special         EMBL flatfiles, all fields indexed
qanxflatexc      N    OK  OK  OK  emboss    -                 special         EMBL flatfiles, no rodent file
qanxflatinc      N    OK  OK  OK  emboss    -                 special         EMBL flatfiles, only rodent file
qanxgcg          N    OK  OK  OK  embossgcg -                 special         GCG format EMBL
qanxgcgall       N    OK  OK  OK  embossgcg sv,des,org,key    special         GCG format EMBL
qanxgcgexc       N    OK  OK  OK  embossgcg -                 special         GCG format EMBL without prokaryotes
qanxgcginc       N    OK  OK  OK  embossgcg -                 special         GCG format EMBL only prokaryotes
qapirexc         N    OK  OK  OK  gcg       -                 special         PIR
qasrswww         N    OK  -   -   srswww    sv,des,org,key    special         Remote SRS web server
qawfasta         N    OK  OK  OK  emblcd    -                 special         FASTA file wormpep entries
qawxfasta        N    OK  OK  OK  emboss    -                 special         FASTA file wormpep entries
qaxpirexc        N    OK  OK  OK  embossgcg -                 special         PIR
tembl            N    OK  OK  OK  emblcd    sv,des,org,key    special 57      EMBL in native format with EMBL CD-ROM index
temblall         N    -   -   OK  direct    sv,des,org,key    special 57      EMBL in native format with EMBL CD-ROM index
temblrest        N    -   -   OK  direct    sv,des,org,key    special 57      EMBL in native format with EMBL CD-ROM index
temblvrt         N    -   -   OK  direct    sv,des,org,key    special 57      EMBL in native format with EMBL CD-ROM index
testdb           N    OK  OK  OK  emblcd    des               special 01      test sequence data
tgb              N    OK  -   -   srswww    sv,des,org,key    special         Genbank IDs
tgenbank         N    OK  OK  OK  emblcd    sv,des,org,key    special 01      GenBank in native format with EMBL CD-ROM index

</pre></td></tr></table><p>
<p>
<p>


<H2>
    Command line arguments
</H2>
<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
   Standard (Mandatory) qualifiers: (none)
   Additional (Optional) qualifiers:
   -database           string     Name of a single database to give
                                  information on (Any string is accepted)
   -html               boolean    [N] Format output as an HTML table
   -[no]protein        boolean    [Y] Display protein databases
   -[no]nucleic        boolean    [Y] Display nucleic acid databases
   -full               boolean    [N] Display all columns
   -methods            boolean    [$(full)] This displays the access methods
                                  that can be used on this database, for all,
                                  query or ID access
   -fields             boolean    [$(full)] This displays the search fields
                                  that can be used on this database, other
                                  than the standard 'id' or 'acc' fields.
   -defined            boolean    [$(full)] This displays a short name for the
                                  file containing the database definition
   -release            boolean    [$(full)] Display 'release' column
   -outfile            outfile    [stdout] Output file name

   Advanced (Unprompted) qualifiers:
   -only               toggle     [N] This is a way of shortening the command
                                  line if you only want a few standard columns
                                  to be displayed. Instead of specifying:
                                  '-nohead -notype -noid -noquery -noall'
                                  to get only the comment output, you can
                                  specify
                                  '-only -comment'
   -heading            boolean    [@(!$(only))] Display column headings
   -type               boolean    [@(!$(only))] Display 'type' column
   -id                 boolean    [@(!$(only))] Display 'id' column
   -query              boolean    [@(!$(only))] Display 'qry' column
   -all                boolean    [@(!$(only))] Display 'all' column
   -comment            boolean    [@(!$(only))] Display 'comment' column

   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write 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. 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

</pre>
</td></tr></table>
<P>

<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Standard (Mandatory) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr>
<td colspan=4>(none)</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Additional (Optional) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr>
<td>-database</td>
<td>Name of a single database to give information on</td>
<td>Any string is accepted</td>
<td><i>An empty string is accepted</i></td>
</tr>

<tr>
<td>-html</td>
<td>Format output as an HTML table</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr>
<td>-[no]protein</td>
<td>Display protein databases</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr>
<td>-[no]nucleic</td>
<td>Display nucleic acid databases</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr>
<td>-full</td>
<td>Display all columns</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr>
<td>-methods</td>
<td>This displays the access methods that can be used on this database, for all, query or ID access</td>
<td>Boolean value Yes/No</td>
<td>$(full)</td>
</tr>

<tr>
<td>-fields</td>
<td>This displays the search fields that can be used on this database, other than the standard 'id' or 'acc' fields.</td>
<td>Boolean value Yes/No</td>
<td>$(full)</td>
</tr>

<tr>
<td>-defined</td>
<td>This displays a short name for the file containing the database definition</td>
<td>Boolean value Yes/No</td>
<td>$(full)</td>
</tr>

<tr>
<td>-release</td>
<td>Display 'release' column</td>
<td>Boolean value Yes/No</td>
<td>$(full)</td>
</tr>

<tr>
<td>-outfile</td>
<td>Output file name</td>
<td>Output file</td>
<td>stdout</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Advanced (Unprompted) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr>
<td>-only</td>
<td>This is a way of shortening the command line if you only want a few standard columns to be displayed. Instead of specifying:
'-nohead -notype -noid -noquery -noall'
to get only the comment output, you can specify
'-only -comment'</td>
<td>Toggle value Yes/No</td>
<td>No</td>
</tr>

<tr>
<td>-heading</td>
<td>Display column headings</td>
<td>Boolean value Yes/No</td>
<td>@(!$(only))</td>
</tr>

<tr>
<td>-type</td>
<td>Display 'type' column</td>
<td>Boolean value Yes/No</td>
<td>@(!$(only))</td>
</tr>

<tr>
<td>-id</td>
<td>Display 'id' column</td>
<td>Boolean value Yes/No</td>
<td>@(!$(only))</td>
</tr>

<tr>
<td>-query</td>
<td>Display 'qry' column</td>
<td>Boolean value Yes/No</td>
<td>@(!$(only))</td>
</tr>

<tr>
<td>-all</td>
<td>Display 'all' column</td>
<td>Boolean value Yes/No</td>
<td>@(!$(only))</td>
</tr>

<tr>
<td>-comment</td>
<td>Display 'comment' column</td>
<td>Boolean value Yes/No</td>
<td>@(!$(only))</td>
</tr>

</table>


<H2>
    Input file format
</H2>

    None.

<p>


<a name="input.3"></a>
<h3>Input files for usage example 3</h3>

'tsw' is a sequence entry in the example protein database 'tsw'
<p>

<H2>
    Output file format
</H2>



<a name="output.2"></a>
<h3>Output files for usage example 2</h3>
<p><h3>File: showdb.out</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
# Name           Type  ID  Qry All Comment
# ============== ==== ==  === === =======
qapblast         P    OK  OK  OK  BLAST swissnew
qapblastall      P    OK  OK  OK  BLAST swissnew, all fields indexed
qapblastsplit    P    OK  OK  OK  BLAST swissnew split in 5 files
qapblastsplitexc P    OK  OK  OK  BLAST swissnew split in 5 files, not file 02
qapblastsplitinc P    OK  OK  OK  BLAST swissnew split in 5 files, only file 02
qapfasta         P    OK  OK  OK  FASTA file swissnew entries
qapflat          P    OK  OK  OK  SpTrEmbl flatfile
qapflatall       P    OK  OK  OK  SpTrEmbl flatfiles, all fields indexed
qapir            P    OK  OK  OK  PIR
qapirall         P    OK  OK  OK  PIR
qapirinc         P    OK  OK  OK  PIR
qapxfasta        P    OK  OK  OK  FASTA file swissnew entries
qapxflat         P    OK  OK  OK  Swissnew flatfiles
qaxpir           P    OK  OK  OK  PIR
qaxpirall        P    OK  OK  OK  PIR
qaxpirinc        P    OK  OK  OK  PIR
tpir             P    OK  OK  OK  PIR using NBRF access for 4 files
tsw              P    OK  OK  OK  Swissprot native format with EMBL CD-ROM index
tswnew           P    OK  OK  OK  SpTrEmbl as 3 files in native format with EMBL CD-ROM index
twp              P    OK  OK  OK  EMBL new in native format with EMBL CD-ROM index
genbanksrs       N    OK  -   -   Genbank IDs
qanfasta         N    OK  OK  OK  FASTA file EMBL rodents
qanfastaall      N    OK  OK  OK  FASTA file EMBL rodents, all fields indexed
qanflat          N    OK  OK  OK  EMBL flatfiles
qanflatall       N    OK  OK  OK  EMBL flatfiles
qanflatexc       N    OK  OK  OK  EMBL flatfiles, no rodent file
qanflatinc       N    OK  OK  OK  EMBL flatfiles, only rodent file
qangcg           N    OK  OK  OK  GCG format EMBL
qangcgall        N    OK  OK  OK  GCG format EMBL
qangcgexc        N    OK  OK  OK  GCG format EMBL without prokaryotes
qangcginc        N    OK  OK  OK  GCG format EMBL only prokaryotes
qanxfasta        N    OK  OK  OK  FASTA file EMBL rodents
qanxfastaall     N    OK  OK  OK  FASTA file EMBL rodents, all fields indexed
qanxflat         N    OK  OK  OK  EMBL flatfiles
qanxflatall      N    OK  OK  OK  EMBL flatfiles, all fields indexed
qanxflatexc      N    OK  OK  OK  EMBL flatfiles, no rodent file
qanxflatinc      N    OK  OK  OK  EMBL flatfiles, only rodent file
qanxgcg          N    OK  OK  OK  GCG format EMBL
qanxgcgall       N    OK  OK  OK  GCG format EMBL
qanxgcgexc       N    OK  OK  OK  GCG format EMBL without prokaryotes
qanxgcginc       N    OK  OK  OK  GCG format EMBL only prokaryotes
qapirexc         N    OK  OK  OK  PIR
qasrswww         N    OK  -   -   Remote SRS web server
qawfasta         N    OK  OK  OK  FASTA file wormpep entries
qawxfasta        N    OK  OK  OK  FASTA file wormpep entries
qaxpirexc        N    OK  OK  OK  PIR
tembl            N    OK  OK  OK  EMBL in native format with EMBL CD-ROM index
temblall         N    -   -   OK  EMBL in native format with EMBL CD-ROM index
temblrest        N    -   -   OK  EMBL in native format with EMBL CD-ROM index
temblvrt         N    -   -   OK  EMBL in native format with EMBL CD-ROM index
testdb           N    OK  OK  OK  test sequence data
tgb              N    OK  -   -   Genbank IDs
tgenbank         N    OK  OK  OK  GenBank in native format with EMBL CD-ROM index
</pre>
</td></tr></table><p>

<p>

The output is a simple table.

<p>

Type 'P' indicates that this is a Protein database.

<p>

Type 'N' indicates that this is a Nucleic database.

<p>

'OK' under ID, Qry or All indicates that that access method can be
used on this database.  A '-' indicates that you cannot access this
database in that way.

<p>

Note that 'OK' does not mean that the database is working correctly.  It
simply means that <b>showdb</b> has read the database definition
correctly and that this method of access to the database should be
possible. 

<p>

If you are setting up a new database, then you should check that it
works correctly by extracting entries from it using <b>seqret</b>. 

<p>

When the -html qualifier is specified, then the output will be wrapped
in HTML tags, ready for inclusion in a Web page.  Note that tags such
as &lt;HTML&gt;, &lt;BODY&gt;, &lt;/BODY&gt; and &lt;/HTML&gt; are not
output by this program as the table of databases is expected to form
only part of the contents of a web page - the rest of the web page
must be supplied by the user.


<H2>
    Data files
</H2>


The databases are specified in the files <i>"emboss.defaults"</i> for
site wide definitions, and <i>"~/.embossrc"</i> for the user's own
settings.
	
<H2>
    Notes
</H2>


Note that 'OK' in the output does not mean that the database is working
correctly.  It simply means that <b>showdb</b> has read the database
definition correctly and that this method of access to the database
should be possible. 

<p>

If you are setting up a new database, then you should check that it
works correctly by extracting entries from it using <b>seqret</b>. 

<p>

You can set up your own private databases by editing a file called
'.embossrc' to contain database specifications. 

<p>

You can set up public databases by editing the file
'/usr/local/share/EMBOSS/emboss.default' (if you have the permission to
do this). 

<p>

The 'emboss.default' file will already have the definitions of the test
databases in: tsw, tembl, tpir, etc.  These are the databases that are
used in the examples shown in the documentation of the programs. 

<p>

For details of the database definitions, you should first read David's
Administration Guide:
<a href="/docs/adminguide/">
http://emboss.sourceforge.net/docs/adminguide/
</a>
especially:
<a href="/docs/adminguide/node4.html">
http://emboss.sourceforge.net/docs/adminguide/adminguide/node4.html
</a>

<p>

See also:
<a href="/docs/themes/Databases.html">
http://emboss.sourceforge.net/docs/themes/Databases.html
</a>
for a lot of detail of the syntax of database definition.

<p>

Just because showdb can display the database definitions, it does NOT
mean that the databases are set up correctly.  You must now test them
using <b>seqret</b>. 


<H2>
    References
</H2>


None.

<H2>
    Warnings
</H2>


None.

<H2>
    Diagnostic Error Messages
</H2>


"The database 'xyz' does not exist" You have supplied the name of a
database with the -database qualifier, but that database does not
exist as far as EMBOSS is concerned.

<H2>
    Exit status
</H2>


It always exits with status 0, unless the above diagnostic message is
displayed.

<H2>
    Known bugs
</H2>


None noted.

<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="abiview.html">abiview</a></td>
<td>Reads ABI file and display the trace</td>
</tr>

<tr>
<td><a href="cirdna.html">cirdna</a></td>
<td>Draws circular maps of DNA constructs</td>
</tr>

<tr>
<td><a href="infoalign.html">infoalign</a></td>
<td>Information on a multiple sequence alignment</td>
</tr>

<tr>
<td><a href="infoseq.html">infoseq</a></td>
<td>Displays some simple information about sequences</td>
</tr>

<tr>
<td><a href="lindna.html">lindna</a></td>
<td>Draws linear maps of DNA constructs</td>
</tr>

<tr>
<td><a href="pepnet.html">pepnet</a></td>
<td>Displays proteins as a helical net</td>
</tr>

<tr>
<td><a href="pepwheel.html">pepwheel</a></td>
<td>Shows protein sequences as helices</td>
</tr>

<tr>
<td><a href="prettyplot.html">prettyplot</a></td>
<td>Displays aligned sequences, with colouring and boxing</td>
</tr>

<tr>
<td><a href="prettyseq.html">prettyseq</a></td>
<td>Output sequence with translated ranges</td>
</tr>

<tr>
<td><a href="remap.html">remap</a></td>
<td>Display sequence with restriction sites, translation etc</td>
</tr>

<tr>
<td><a href="seealso.html">seealso</a></td>
<td>Finds programs sharing group names</td>
</tr>

<tr>
<td><a href="showalign.html">showalign</a></td>
<td>Displays a multiple sequence alignment</td>
</tr>

<tr>
<td><a href="showfeat.html">showfeat</a></td>
<td>Show features of a sequence</td>
</tr>

<tr>
<td><a href="showseq.html">showseq</a></td>
<td>Display a sequence with features, translation etc</td>
</tr>

<tr>
<td><a href="sixpack.html">sixpack</a></td>
<td>Display a DNA sequence with 6-frame translation and ORFs</td>
</tr>

<tr>
<td><a href="textsearch.html">textsearch</a></td>
<td>Search sequence documentation. Slow, use SRS and Entrez!</td>
</tr>

<tr>
<td><a href="tfm.html">tfm</a></td>
<td>Displays a program's help documentation manual</td>
</tr>

<tr>
<td><a href="whichdb.html">whichdb</a></td>
<td>Search all databases for an entry</td>
</tr>

<tr>
<td><a href="wossname.html">wossname</a></td>
<td>Finds programs by keywords in their one-line documentation</td>
</tr>

</table>

<H2>
    Author(s)
</H2>
Gary Williams (gwilliam&nbsp;&copy;&nbsp;rfcgr.mrc.ac.uk)
<br>
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK



<H2>
    History
</H2>

Completed 6th August 1999.

<H2>
    Target users
</H2>
This program is intended to be used by everyone and everything, from naive users to embedded scripts.

<H2>
    Comments
</H2>
None

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</HTML>