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 It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal and sequence data.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

       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

       Associated qualifiers:
      "-outfile" related 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 required and optional values
       -debug               boolean    Write debug output to program.dbg
       -acdlog              boolean    Write ACD processing log to program.acdlog
       -acdpretty           boolean    Rewrite ACD file as program.acdpretty
       -acdtable            boolean    Write HTML table of options
       -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

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) | 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

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
--- | ---
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 © hgmp.mrc.ac.uk)
HGMP-RC, 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