first previous next last contents

Restriction Enzyme File

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 roberts@neb.com or macelis@neb.com to join the mailing list and state that you want the files sent in "staden" format.

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 in order to correctly show the cutting 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//

first previous next last contents
This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/formats_16.html