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.
It will also (by default) produce an 'embossre.equ' file. This can be turned off by setting the -equivalences option to be false. This option calculates an 'embossre.equ' file using restriction enzyme prototypes in the "withrefm" file. The 'embossre.equ' file is a file of preferred isoschizomers. You may edit it to contain your available restriction enzymes.
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.
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For example, the withrefm file for REBASE version 005 is at: ftp://ftp.neb.com/pub/rebase/withrefm.005
The output files are held in the REBASE subdirectory of the EMBOSS data directory. There are three:
rebaseextract will also (by default) produce an 'embossre.equ' file in the EMBOSS data directory. This can be turned off by setting the -equivalences option to be false. This option calculates an 'embossre.equ' file using restriction enzyme prototypes in the "withrefm" file. The 'embossre.equ' file is a file of preferred isoschizomers. You may edit it to contain your available restriction enzymes.
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