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 It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal and sequence data.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

- . (your current directory)
- .embossdata (under your current directory)
- ~/ (your home directory)
- ~/.embossdata

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:

- 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

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
--- | ---
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 - Alan Bleasby

## Target users

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

## Comments

None