RESTRICTION ENDONUCLEASE DIGESTION

BACKGROUND INFORMATION: General review (Promega),  General review (P. McClean); Type I Restriction-Modification Systems (K. Firman, University of Portsmouth), 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.

red_bullet.gif (914 bytes) Webcutter 2.0 (U.S.A.)
red_bullet.gif (914 bytes) WatCut (Michael Palmer, University of Waterloo, Canada) - provides restriction analysis coupled with where the sites are located within genes.  
red_bullet.gif (914 bytes) Restriction Site Analysis - (University of Massachusetts Medical School, U.S,A.) uses H. Mangalam's TACG2 program. Provides one with considerable choice of enzymes and output format, including pseudo gel maps. 

red_bullet.gif (914 bytes) Restriction Enzyme Picker (G. Rocap & E. Collins, School of Oceanography, University of Washington, U.S.A.) - finds sets of 4 commercially available restriction endonucleases which together uniquely differentiate designated sequence groups from a supplied FASTA format sequence file for use in T-RFLP.

red_bullet.gif (914 bytes) 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.

red_bullet.gif (914 bytes) Other restriction sites include Restriction enzyme digest of DNA, RestrictionMapper ,   Restriction Map, and Restriction Digest.

red_bullet.gif (914 bytes) 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.

red_bullet.gif (914 bytes) 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).

red_bullet.gif (914 bytes) 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.