EMBOSS: rebaseextract

| ## EMBOSS: rebaseextract

# Program rebaseextract

## Function

Extract data from REBASE

## 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 It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal and sequence data.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 derives recognition site and cleavage information from the "withrefm" file of an REBASE distribution. It creates three files in the EMBOSS data subdirectory REBASE. A pattern file, a reference file and a supplier file.

The EMBOSS programs that find restriction cutting sites use the data files produced by this program and will not work without them.

Running this program may be the job of your system manager.

## Usage

Here is a sample session with rebaseextract.

    % rebaseextract
    Full pathname of WITHREFM: /data/rebase/withrefm.904

## Command line arguments

       Mandatory qualifiers:
      [-inf]               infile     Full pathname of WITHREFM

       Optional qualifiers: (none)
       Advanced qualifiers: (none)
       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
--- | --- | ---
[-inf] (Parameter 1) | Full pathname of WITHREFM | Input file | Required
Optional qualifiers | Allowed values | Default
(none)
Advanced qualifiers | Allowed values | Default
(none)

## Input file format

The input file must be the "withrefm" file of a REBASE distribution.

For example, the withrefm file for REBASE version 005 is at: ftp://ftp.neb.com/pub/rebase/withrefm.005

## Output file format

The output files are held in the REBASE subdirectory of the EMBOSS data directory. There are three:

- embossre.enz Enzyme pattern file
- embossre.ref Enzyme references
- embossre.sup Enzyme suppliers

Here are examples of the three formats:

- a) Enzyme file

      #             length  cuts     blunt    3'      5'     [3']    [5']
      AlwI    GGATC   5       2       0       9       10      0       0
      Alw21I  GWGCWC  6       2       0       5       1       0       0
      Alw26I  GTCTC   5       2       0       6       10      0       0
      Alw44I  GTGCAC  6       2       0       1       5       0       0

- b) Reference file

      # REBASE enzyme information for EMBOSS
      #
      # Format:
      # Line 1: Name of Enzyme
      # Line 2: Organism
      # Line 3: Isoschizomers
      # Line 4: Methylation
      # Line 5: Source
      # Line 6: Suppliers
      # Line 7: Number of following references
      # Lines 8..n: References
      # // (end of entry marker)
      #
      AclI
      Acinetobacter calcoaceticus M4
      Psp1406I
      ?(5)
      S.K. Degtyarev
      IN
      1
      Nucleic Acids Res. vol. 20 pp. 3787.
      //

- c) Suppliers file

      # REBASE Supplier information for EMBOSS
      #
      # Format:
      # Code of Supplier<ws>Supplier name
      #
      A Amersham Pharmacia Biotech (11/98)
      B Life Technologies Inc. (1/98)
      C Minotech, Molecular Biology Products (3/99)
      D Angewandte Gentechnologie Systeme (10/97)
      E Stratagene (1/98)
      F Fermentas AB (1/99)
      G Appligene Oncor (10/97)
      H American Allied Biochemical, Inc. (10/98)
      I SibEnzyme Ltd. (3/99)
      J Nippon Gene Co., Ltd. (10/97)
      K Takara Shuzo Co. Ltd. (11/98)
      L Kramel Biotech (7/98)
      M Roche Molecular Biochemicals (3/99)
      N New England BioLabs (3/99)
      O Toyobo Biochemicals (11/98)
      P Megabase Research Products (3/99)
      Q CHIMERx (10/97)
      R Promega Corporation (10/98)
      S Sigma Chemical Corporation (11/98)
      T Advanced Biotechnologies Ltd. (3/98)

## Data files

The "withrefm" file of an REBASE distribution is the input file for this program.

## Notes

The home page of REBASE is: http://rebase.neb.com/

Running this program may be the job of your system manager.

The ready-made files produced by this program may already be available at the REBASE web site: http://rebase.neb.com/rebase/rebase.files.html or http://rebase.neb.com/rebase/rebase.f37.html

## References

1. Nucleic Acids Research 27: 312-313 (1999).

## Warnings

The program will warn you if the input file is incorrectly formatted.

## Diagnostic Error Messages

## Exit status

It exits with status 0 unless an error is reported.

## Known bugs

## See also

Program name | Description
--- | ---
cutgextract | Extract data from CUTG
domainer | Build domain coordinate files
nrscope | Converts redundant EMBL-format SCOP file to non-redundant one
pdbtosp | Convert raw swissprot:pdb equivalence file to embl-like format
printsextract | Extract data from PRINTS
prosextract | Builds the PROSITE motif database for patmatmotifs to search
scope | Convert raw scop classification file to embl-like format
scopparse | Reads raw-, and writes EMBL-like, scop classification files
seqnr | Converts redundant database results to a non-redundant set of hits
tfextract | Extract data from TRANSFAC

## Author(s)

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

## History

Completed 12th April 1999

## Target users

This program is intended to be used by administrators responsible for software and database installation and maintenance.

## Comments