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<HTML>

<HEAD>
  <TITLE>
  EMBOSS: redata
  </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">
redata
</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>
Retrieve information from REBASE restriction enzyme database

<H2>
    Description
</H2>


<p><b>redata</b> searches the REBASE database for information on a specified restriction enzyme. It writes an output file with information on the cut site and (optionally) the full list of isoschizomers (enzymes with the same target sequence), commercial suppliers of the enzyme and literature references.</p>

<H2>
    Usage
</H2>
Here is a sample session with <b>redata</b>
<p>

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

% <b>redata </b>
Retrieve information from REBASE restriction enzyme database
Restriction enzyme name [BamHI]: <b>BamHI</b>
Output file [outfile.redata]: <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>
Retrieve information from REBASE restriction enzyme database
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-enzyme]            string     [BamHI] Enter the name of the restriction
                                  enzyme that you wish to get details of. The
                                  names often have a 'I' in them - this is a
                                  capital 'i', not a '1' or an 'l'. The names
                                  are case-independent ('AaeI' is the same as
                                  'aaei') (Any string)
  [-outfile]           outfile    [*.redata] Output file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -[no]isoschizomers  boolean    [Y] Show other enzymes with this
                                  specificity. (Isoschizomers)
   -[no]references     boolean    [Y] Show references
   -[no]suppliers      boolean    [Y] Show suppliers

   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory

   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>[-enzyme]<br>(Parameter 1)</td>
<td>string</td>
<td>Enter the name of the restriction enzyme that you wish to get details of. The names often have a 'I' in them - this is a capital 'i', not a '1' or an 'l'. The names are case-independent ('AaeI' is the same as 'aaei')</td>
<td>Any string</td>
<td>BamHI</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-outfile]<br>(Parameter 2)</td>
<td>outfile</td>
<td>Output file name</td>
<td>Output file</td>
<td><i>&lt;*&gt;</i>.redata</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>-[no]isoschizomers</td>
<td>boolean</td>
<td>Show other enzymes with this specificity. (Isoschizomers)</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-[no]references</td>
<td>boolean</td>
<td>Show references</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-[no]suppliers</td>
<td>boolean</td>
<td>Show suppliers</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

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

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

<tr bgcolor="#FFFFCC">
<td> -odirectory2<br>-odirectory_outfile</td>
<td>string</td>
<td>Output directory</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>



<H2>
    Output file format
</H2>



<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: outfile.redata</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
BamHI

Recognition site is GGATCC leaving sticky ends
  Cut positions 5':1 3':5
Organism: Bacillus amyloliquefaciens H
Methylated: 5(4)
Source: ATCC 49763

Isoschizomers:
   AacI        AaeI        AcaII       AccEBI      AinII       AliI        
   Ali12257I   Ali12258I   ApaCI       AsiI        AspTII      Atu1II      
   BamFI       BamKI       BamNI       Bca1259I    Bce751I     Bco10278I   
   BnaI        BsaDI       Bsp30I      Bsp46I      Bsp90II     Bsp98I      
   Bsp130I     Bsp131I     Bsp144I     Bsp4009I    BspAAIII    BstI        
   Bst1126I    Bst2464I    Bst2902I    BstQI       Bsu90I      Bsu8565I    
   Bsu8646I    BsuB519I    BsuB763I    CelI        DdsI        GdoI        
   GinI        GoxI        GseIII      MleI        Mlu23I      NasBI       
   Nsp29132II  NspSAIV     OkrAI       Pac1110I    Pae177I     Pfl8I       
   Psp56I      RhsI        Rlu4I       RspLKII     SolI        SpvI        
   SurI        Uba19I      Uba31I      Uba38I      Uba51I      Uba88I      
   Uba1098I    Uba1163I    Uba1167I    Uba1172I    Uba1173I    Uba1205I    
   Uba1224I    Uba1242I    Uba1250I    Uba1258I    Uba1297I    Uba1302I    
   Uba1324I    Uba1325I    Uba1334I    Uba1339I    Uba1346I    Uba1383I    
   Uba1398I    Uba1402I    Uba1414I    

Suppliers:
Amersham Pharmacia Biotech (1/01)
Life Technologies Inc. (1/98)
Minotech, Molecular Biology Products (12/00)
HYBAID GmbH (12/00)
Stratagene (11/00)
Fermentas AB (5/01)
Q-BIOgene (1/01)
American Allied Biochemical, Inc. (10/98)
SibEnzyme Ltd. (1/01)
Nippon Gene Co., Ltd. (6/00)
Takara Shuzo Co. Ltd. (2/01)
Transgenomic Ltd. (1/01)
Roche Molecular Biochemicals (1/01)
New England BioLabs (12/00)
Toyobo Biochemicals (11/98)
CHIMERx (10/97)
Promega Corporation (6/99)
Sigma Chemical Corporation (11/98)
Advanced Biotechnologies Ltd. (3/98)
Bangalore Genei (2/01)
MRC-Holland (3/01)

References:
Brooks, J.E., Howard, K.A., US Patent Office, 1994.
Brooks, J.E., Nathan, P.D., Landry, D., Sznyter, L.A., Waite-Rees, P., Ives, C.L., Moran, L.S., Slatko, B.E., Benner, J.S., (1991) Nucleic Acids Res., vol. 19, pp. 841-850.
Hattman, S., Keister, T., Gottehrer, A., (1978) J. Mol. Biol., vol. 124, pp. 701-711.
Lee, S.P., Porter, D., Chirikjian, J.G., Knutson, J.R., Han, M.K., (1994) Anal. Biochem., vol. 220, pp. 377-383.
Newman, M., Strzelecka, T., Dorner, L.F., Schildkraut, I., Aggarwal, A.K., (1994) Structure, vol. 2, pp. 439-452.
Roberts, R.J., Wilson, G.A., Young, F.E., (1977) Nature, vol. 265, pp. 82-84.
Roy, K.B., Vrushank, D., Jayaram, B., (1994) Anal. Biochem., vol. 220, pp. 160-164.
Strzelecka, T., Newman, M., Dorner, L.F., Knott, R., Schildkraut, I., Aggarwal, A.K., (1994) J. Mol. Biol., vol. 239, pp. 430-432.
Wilson, G.A., Young, F.E., (1975) J. Mol. Biol., vol. 97, pp. 123-125.
Xu, S.-Y., Fomenkov, A., (1994) Biotechniques, vol. 17, pp. 57.
</pre>
</td></tr></table><p>

<p>

This includes the full list of isoschizomers (enzymes with the same
target sequence), suppliers and references from the REBASE database. 

<H2>
    Data files
</H2>

<p>
EMBOSS data files are distributed with the application and stored
in the standard EMBOSS data directory, which is defined
by the EMBOSS environment variable EMBOSS_DATA.

<p>

To see the available EMBOSS data files, run:
<p>
<pre>
% embossdata -showall
</pre>
<p>
To fetch one of the data files (for example 'Exxx.dat') into your
current directory for you to inspect or modify, run:

<pre>

% embossdata -fetch -file Exxx.dat

</pre>
<p>

Users can provide their own data files in their own directories.
Project specific files can be put in the current directory, or for
tidier directory listings in a subdirectory called
".embossdata". Files for all EMBOSS runs can be put in the user's home
directory, or again in a subdirectory called ".embossdata".

<p>
The directories are searched in the following order:

<ul>
   <li> . (your current directory)
   <li> .embossdata (under your current directory)
   <li> ~/ (your home directory)
   <li> ~/.embossdata
</ul>
<p>
<p>
The EMBOSS REBASE restriction enzyme data files are stored in
directory 'data/REBASE/*' under the EMBOSS installation directory.

<p>

These files must first be set up using the program <a
href="rebaseextract.html">'<b>rebaseextract</b>'</a>.  Running
'rebaseextract' may be the job of your system manager.

<p>
      
The data files are stored in the REBASE directory of the standard EMBOSS
data directory. The names are:

<ul>
<li> embossre.enz     Cleavage information
<li> embossre.ref     Reference/methylation information
<li> embossre.sup     Supplier information
</ul>
	 
The column information is described at the top of the data files
	 
<p>
	 
The reported enzyme from any one group of isoschizomers (the prototype)
is specified in the REBASE database and the information is held in the
data file 'embossre.equ'.  You may edit this file to set your own
preferred prototype, if you wish. 
	 
<p>
	 
The format of the file "embossre.equ" is
<br>
Enzyme-name Prototype-name
	 
<p>
	 
i.e.  two columns of enzyme names separated by a space.  The first name
of the pair of enzymes is the name that is not preferred and the second
is the preferred (prototype) name. 
	 
	          

<H2>
    Notes
</H2>

<p>The Restriction Enzyme database (REBASE) is a collection of information about restriction enzymes and related proteins. It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal and sequence data. DNA methyltransferases, homing endonucleases, nicking enzymes, specificity subunits and control proteins are also included. More recently, putative DNA methyltransferases and restriction enzymes, as predicted from analysis of genomic sequences, are also listed.</p>

<p>The home page of REBASE is: <a href="http://rebase.neb.com/">http://rebase.neb.com/</a></p>

<H2>
    References
</H2>

None.

<H2>
    Warnings
</H2>

<p><b>redata</b> uses the EMBOSS REBASE restriction enzyme data files stored in directory <tt>data/REBASE/*</tt> under the EMBOSS installation directory. These files must first be set up using the program <b>rebaseextract</b>. Running <b>rebaseextract</b> may be the job of your system manager.</p>

<H2>
    Diagnostic Error Messages
</H2>

None.

<H2>
    Exit status
</H2>

It always exits with a status of 0.

<H2>
    Known bugs
</H2>


None.

<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="recoder.html">recoder</a></td>
<td>Find restriction sites to remove (mutate) with no translation change</td>
</tr>

<tr>
<td><a href="remap.html">remap</a></td>
<td>Display restriction enzyme binding sites in a nucleotide sequence</td>
</tr>

<tr>
<td><a href="restover.html">restover</a></td>
<td>Find restriction enzymes producing a specific overhang</td>
</tr>

<tr>
<td><a href="restrict.html">restrict</a></td>
<td>Report restriction enzyme cleavage sites in a nucleotide sequence</td>
</tr>

<tr>
<td><a href="showseq.html">showseq</a></td>
<td>Display sequences with features in pretty format</td>
</tr>

<tr>
<td><a href="silent.html">silent</a></td>
<td>Find restriction sites to insert (mutate) with no translation change</td>
</tr>

</table>

<H2>
    Author(s)
</H2>


Alan Bleasby 
<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>

Written 1999 - Alan Bleasby

<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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