rebaseextract processes the REBASE database for use by the EMBOSS restriction enzyme applications. It 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 of preferred isoschizomers using restriction enzyme prototypes in the "proto" file. This can be turned off by setting the -equivalences option to be false.
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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.
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 It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal and sequence data.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/
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.
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
You may edit the embossre.equ file it to contain details for your available restriction enzymes.