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 It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal and sequence data.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]: 
Output file [outfile.redata]: 

Command line arguments

   Mandatory qualifiers:
  [-enzyme]            string     Enter the name of the restrcition 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-indeppendent ('AaeI' is the same as
                                  'aaei')
  [-outfile]           outfile    Output file name

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

   General qualifiers:
  -help                boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose


Mandatory qualifiers Allowed values Default
[-enzyme]
(Parameter 1)
Enter the name of the restrcition 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-indeppendent ('AaeI' is the same as 'aaei') Any string is accepted BamHI
[-outfile]
(Parameter 2)
Output file name Output file <sequence>.redata
Optional qualifiers Allowed values Default
(none)
Advanced qualifiers Allowed values Default
-[no]isoschizomers Show other enzymes with this specificity. (Isoschizomers) Yes/No Yes
-[no]references Show references Yes/No Yes
-[no]suppliers Show suppliers Yes/No Yes

Input file format

Output file format

Here is the output from the example run. It includes the full list of isoschizomers (enzymes with the same target sequence), suppliers and references from the REBASE database.

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     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 (11/98)
Life Technologies Inc. (1/98)
Minotech, Molecular Biology Products (3/99)
Angewandte Gentechnologie Systeme (10/97)
Stratagene (1/98)
Fermentas AB (8/99)
Appligene Oncor (10/97)
American Allied Biochemical, Inc. (10/98)
SibEnzyme Ltd. (9/99)
Nippon Gene Co., Ltd. (10/97)
Takara Shuzo Co. Ltd. (11/98)
Kramel Biotech (7/98)
Roche Molecular Biochemicals (3/99)
New England BioLabs (2/00)
Toyobo Biochemicals (11/98)
CHIMERx (10/97)
Promega Corporation (6/99)
Sigma Chemical Corporation (11/98)
Advanced Biotechnologies Ltd. (3/98)

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.

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

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Program nameDescription
recoderRemove restriction sites but maintain the same translation
remapDisplay a sequence with restriction cut sites, translation etc
restoverFinds restriction enzymes that produce a specific overhang
restrictFinds restriction enzyme cleavage sites
showseqDisplay a sequence with features, translation etc
silentSilent mutation restriction enzyme scan

Author(s)

This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)

History

Target users

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

Comments