Restriction enzymes and their recognition sequences used by the package must be stored in the format described below. Updates of the files can be obtained from the REBASE restriction enzyme database of Dr R Roberts. Contact firstname.lastname@example.org or email@example.com to join the mailing list and state that you want the files sent in "staden" format.
Standard four-cutter, six-cutter and all-enzymes files are supplied with the package and users can create and use their own "personal" files. To create your own file of enzymes you may need to extract the information from the currently defined files. These are stored in the tables directory (folder) distributed with the package, and are named:
RENZYM.4 RENZYM.6 RENZYM.ALL
We call the recognition sequences "strings". The format is as follows: each string or set of strings must be preceded by a name, each string must be preceded and terminated with a slash (/), and each set of strings by 2 slashes. For example AATII/GACGT'C// defines the name AATII, its recognition sequence GACGTC and its cut site with the ' symbol; ACCI/GT'MKAC// defines the name ACCI and its recognition sequence includes IUB symbols for incompletely defined symbols in nucleic acid sequences; BBVI/GCAGCNNNNNNNN'/'NNNNNNNNNNNNGCTGC// defines the name BBVI and this time two recognition sequences and cut sites are specified to enable the definition of the cut position relative to the recognition sequence. If no cut site is included the first base of the recognition sequence is displayed as being on the 3' side of the recognition sequence.
A section of a typical file follows:
AATII/GACGT'C// ACCI/GT'MKAC// AFLII/C'TTAAG// AVAII/G'GWCC// AVRII/C'CTAGG// BANI/G'GYRCC// BANII/GRGCY'C// BBVI/GCAGCNNNNNNNN'/'NNNNNNNNNNNNGCTGC// BCLI/T'GATCA// BGLI/GCCNNNN'NGGC// BGLII/A'GATCT// BINI/GGATCNNNN'/'NNNNNGATCC// BSMI/GAATGCN'/NG'CATTC// BSP1286/GDGCH'C//