                                   redata



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Function

   Retrieve information from REBASE restriction enzyme database

Description

   redata 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.

Usage

   Here is a sample session with redata


% redata
Retrieve information from REBASE restriction enzyme database
Restriction enzyme name [BamHI]: BamHI
Output file [outfile.redata]:


   Go to the output files for this example

Command line arguments

Retrieve information from REBASE restriction enzyme database
Version: EMBOSS:6.5.6.0

   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


Input file format

Output file format

  Output files for usage example

  File: outfile.redata

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. 160-1
64.
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.

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

Data files

   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.

   To see the available EMBOSS data files, run:

% embossdata -showall

   To fetch one of the data files (for example 'Exxx.dat') into your
   current directory for you to inspect or modify, run:

% embossdata -fetch -file Exxx.dat


   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".

   The directories are searched in the following order:
     * . (your current directory)
     * .embossdata (under your current directory)
     * ~/ (your home directory)
     * ~/.embossdata

   The EMBOSS REBASE restriction enzyme data files are stored in directory
   'data/REBASE/*' under the EMBOSS installation directory.

   These files must first be set up using the program 'rebaseextract'.
   Running 'rebaseextract' may be the job of your system manager.

   The data files are stored in the REBASE directory of the standard
   EMBOSS data directory. The names are:
     * embossre.enz Cleavage information
     * embossre.ref Reference/methylation information
     * embossre.sup Supplier information

   The column information is described at the top of the data files

   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.

   The format of the file "embossre.equ" is
   Enzyme-name Prototype-name

   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.

Notes

   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.

   The home page of REBASE is: http://rebase.neb.com/

References

   None.

Warnings

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

Diagnostic Error Messages

   None.

Exit status

   It always exits with a status of 0.

Known bugs

   None.

See also

   Program name     Description
   recoder          Find restriction sites to remove (mutate) with no translation
                    change
   remap            Display restriction enzyme binding sites in a nucleotide sequence
   restover         Find restriction enzymes producing a specific overhang
   restrict         Report restriction enzyme cleavage sites in a nucleotide
                    sequence
   showseq          Display sequences with features in pretty format
   silent           Find restriction sites to insert (mutate) with no translation
                    change

Author(s)

   Alan Bleasby
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) not to the original author.

History

   Written 1999 - Alan Bleasby

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments

   None
