Enzymes¶

List of commonly used restriction enzymes and the required parameters to use them with ddRAGE:

Name	Type	Recognition Sequence	Residue
Csp6I	Frequent	GTAC	TAC
PstI	Frequent	CTGCAG	G

NsiI	Rare	ATGCAT	TGCAT
BamHI	Rare	GGATCC	GATCC

FatI		CATG
NlaIII		GATG
MluCI		AATT
EcoRI		GAATTC	ATTC
MspI		CCGG	CGG
SbfI		CCTGCAGG	GG

The recognition sequence needs to be passed to the --p5/p7-rec-site parameter and the residue to the --p5/p7-overhang parameter. Example:

me@machine:~$ ddrage --p5-rec-site GGATCC --p5-overhang GATCC --p7-rec-site GTAC --p7-overhang TAC

Use BamHI as rare cutter and Csp6I as frequent cutter.