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 2.0 (U.S.A.)
WatCut (Michael Palmer, University of Waterloo, Canada) - provides restriction analysis coupled with where the sites are located within genes.
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.
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.
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.
Restriction Comparator (Vladimír Cermák, molbiotools.com) - Carry out parallel in silico restriction analysis online. Compare two sequences side by side. Find distinguishing restriction sites. Visualize restriction patterns.
WebDSV (Vladimír Cermák, molbiotools.com) - is a basic molecular biology app to create, edit and analyze DNA sequences, mark and visualize sequence features, and generate plasmid maps. With WebDSV you can analyze restriction sites, perform in silico molecular cloning, and design PCR primers.
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.