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 It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal and sequence data.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. 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.

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:

The EMBOSS REBASE restriction enzyme data files are stored iin 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:

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

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 nameDescription
recoderRemove restriction sites but maintain same translation
remapDisplay sequence with restriction sites, translation etc
restoverFind restriction enzymes producing specific overhang
restrictFinds restriction enzyme cleavage sites
showseqDisplay a sequence with features, translation etc
silentSilent mutation restriction enzyme scan

Author(s)

Alan Bleasby (ajb © ebi.ac.uk)
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

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