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.
This analysis can also be undertaken at
tacg V3.5.
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.
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.
S equence
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.
If you are thinking about cloning be
sure to visit CloneIt!
(Pierre Lindenbaum, Institut National de la Recherche
Agronomique, France) an
online program finding
sub-cloning strategies, in-frame deletions and frameshift using
restriction enzymes and DNA
polymerase. The number of clones required to
cover the DNA can be calculated using Physical
mapping calculator -
library construction (Andrei
Grigoriev).