EMBOSS: redata

| ## EMBOSS: redata

# Program 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 It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal and sequence data.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  bool       Show other enzymes with this specificity.
                                      (Isoschizomers)
       -[no]references     bool       Show references
       -[no]suppliers      bool       Show suppliers

       General qualifiers:
      -help                bool       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 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)

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