NEBcutter
On-line DNA sequence tool to find large, non-overlapping, open reading frames and sites for all restriction enzymes-from New England BioLabs.
REBASE
The restriction enzyme database, from New England Biolabs.
WatCut
Watcut is an on-line tool that offers three functions: 1. restriction mapping, 2. silent mutation scanning, and 3. scanning for amplification-created restriction sites that facilitate detection of SNP by PCR.
Webcutter 2.0
Free, online software for restriction mapping nucleotide sequences.