RESTRICTION ENDONUCLEASE DIGESTION
BACKGROUND INFORMATION: General review (Promega), General review (P. McClean); Gene Infinity (good meta source)
SITES: Though I favour Webcutter 2.0 and WatCut for their simplicity all of these sites are well worthwhile visiting.
Webcutter (Max Heiman, U.S.A.). Can also be found here.
WatCut (Michael Palmer, University of Waterloo, Canada) - provides restriction analysis coupled with where the sites are located within genes.
RFLP enzyme picker - This web page is designed to find restriction enzymes that cut one variant but no the other of a polymorphic site. The program looks for restriction sites that contain the variant base (identified by the use of an IUPAC 1-letter code abbreviation) in the input sequence.
NEBcutter (New England Biolabs, U.S.A.) - provides opportunities to upload local files, choose from common vector sequences or enter GenBank accession numbers. Also includes ability to map sites in genes. After you have the restriction map for this sequence you might want to consult the New England Biolabs (U.S.A.) site: The Restriction Enzyme Database for specifics on each restriction endonuclease and its availability.
Other restriction sites include Restriction enzyme digest of DNA, RestrictionMapper, Restriction Map, and Restriction Digest.
Restriction Analyzer (Vladimír Cermák, molbiotools.com) - carry out in silico restriction analysis online. Quickly find absent and unique sites. Tabular and graphical output. Analyze restriction fragments. Simulate a gel electrophoresis.
In silico restriction digest of complete genomes (University of the Basque Country, Spain) - allows in silico digestion of over 300 prokaryotic genomes and simulated pulsed-field gel electrophoretic separation of the fragments.
Computation of size of DNA and Protein Fragments from Their Electrophoretic Mobility (Reference: Raghava, G. P. S. 2001. Biotech Software and Internet Report 2:198-200).
Sequence Extractor (Paul Stothard) - generates a clickable restriction map and PCR primer map of a DNA sequence (accepted formats are: raw, GenBank, EMBL, and FASTA) offering a great deal of control on output. Protein translations and intron/exon boundaries are also shown. Use Sequence Extractor to build DNA constructs in silico.