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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="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>
<p>
<H2>
Function
</H2>
Search REBASE for enzyme name, references, suppliers etc
<H2>
Description
</H2>
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unpublished references, recognition and cleavage sites, isoschizomers,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. Most recently, putative DNA
methyltransferases and restriction enzymes, as predicted from analysis of
genomic sequences, are also listed.
<p>
The home page of REBASE is: <a
href="http://rebase.neb.com/">http://rebase.neb.com/</a>
<p>
This program searches the REBASE database for information on a specified
restriction enzyme.
<p>
It outputs a report including the cut site, isoschizomers, references
and commercial suppliers of the enzyme.
<H2>
Usage
</H2>
<b>Here is a sample session with redata</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>redata </b>
Search REBASE for enzyme name, references, suppliers etc.
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>
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 is accepted)
[-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 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>[-enzyme]<br>(Parameter 1)</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 is accepted</td>
<td>BamHI</td>
</tr>
<tr>
<td>[-outfile]<br>(Parameter 2)</td>
<td>Output file name</td>
<td>Output file</td>
<td><i><*></i>.redata</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 colspan=4>(none)</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>-[no]isoschizomers</td>
<td>Show other enzymes with this specificity. (Isoschizomers)</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>
<tr>
<td>-[no]references</td>
<td>Show references</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>
<tr>
<td>-[no]suppliers</td>
<td>Show suppliers</td>
<td>Boolean value Yes/No</td>
<td>Yes</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 iin
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>
None.
<H2>
References
</H2>
None.
<H2>
Warnings
</H2>
None.
<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>Remove restriction sites but maintain same translation</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="restover.html">restover</a></td>
<td>Find restriction enzymes producing specific overhang</td>
</tr>
<tr>
<td><a href="restrict.html">restrict</a></td>
<td>Finds restriction enzyme cleavage sites</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="silent.html">silent</a></td>
<td>Silent mutation restriction enzyme scan</td>
</tr>
</table>
<H2>
Author(s)
</H2>
Alan Bleasby (ajb © ebi.ac.uk)
<br>
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
<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
</BODY>
</HTML>
|
