
                                  redata 
                                      
   
   
Function

   Search REBASE for enzyme name, references, suppliers etc
   
Description

   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   contains published and unpublished references, recognition and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.
   
   The home page of REBASE is: http://rebase.neb.com/
   
   This program searches the REBASE database for information on a
   specified restriction enzyme.
   
   It outputs a report including the cut site, isoschizomers, references
   and commercial suppliers of the enzyme.
   
Usage

   Here is a sample session with redata
   

% redata 
Search REBASE for enzyme name, references, suppliers etc.
Restriction enzyme name [BamHI]: BamHI
Output file [outfile.redata]: 
   
   Go to the output files for this example
   
Command line arguments

   Standard (Mandatory) qualifiers:
  [-enzyme]            string     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')
  [-outfile]           outfile    Output file name

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

   Standard (Mandatory) qualifiers Allowed values Default
   [-enzyme]
   (Parameter 1) 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 BamHI
   [-outfile]
   (Parameter 2) Output file name Output file <sequence>.redata
   Additional (Optional) qualifiers Allowed values Default
   (none)
   Advanced (Unprompted) qualifiers Allowed values Default
   -[no]isoschizomers Show other enzymes with this specificity.
   (Isoschizomers) Boolean value Yes/No Yes
   -[no]references Show references Boolean value Yes/No Yes
   -[no]suppliers Show suppliers Boolean value Yes/No Yes
   
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. 70
1-711.
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., (199
4) 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.
   
   This includes the full list of isoschizomers (enzymes with the same
   target sequence), suppliers and references from the REBASE database.
   
Data files

   This uses the EMBOSS REBASE data files in '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.
   
Notes

   None.
   
References

   None.
   
Warnings

   None.
   
Diagnostic Error Messages

   None.
   
Exit status

   It always exits with a status of 0.
   
Known bugs

   None.
   
See also

   Program name                          Description
   recite       Find changes to an enzyme site that introduce new enzyme sites
   recoder      Remove restriction sites but maintain the same translation
   remap        Display a sequence with restriction cut sites, translation etc
   restover     Finds restriction enzymes that produce a specific overhang
   restrict     Finds restriction enzyme cleavage sites
   showseq      Display a sequence with features, translation etc
   silent       Silent mutation restriction enzyme scan
   
Author(s)

   Alan Bleasby (ableasby © rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
   
History

   Written 1999.
   
Target users

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