Research Tools

• NEBcutter (New England Biolabs)
  This tool will take a DNA sequence and find the large, non-overlapping open reading frames and the sites for all restriction enzymes that cut the sequence just once. By default, only enzymes available from NEB are used, but other sets may be chosen. Just enter your sequence and "submit". Further options will appear with the output.
  http://tools.neb.com/NEBcutter/index.php3
  Added: Sun Jul 21 2002, Hits: 5894, Reviews: 0  Write review   Cached
• Cutter (Pierre Rodrigues, JustBio)
  With this tool you can quicky get the list of all enzyme restriction sites on your sequence. (Free registration needed)
  http://www.justbio.com/cutter/index.php
  Added: Sun Aug 18 2002, Hits: 3110, Reviews: 0  Write review   Cached
• Restriction enzyme digest of complete genomes and PFGE (University of The Basque Country)
  This sites shows number of times each commercial endonuclease cleaves up-to-dated secuenced bacterial genomes (over 200). When this number is bellow 50, Pulsed Field Gel Electrphresis is simulated.
  http://www.in-silico.com/s_digest/info.html
  Added: Wed Jan 26 2005, Hits: 740, Reviews: 0  Write review   Cached
• Restriction Enzyme Digest of DNA (Dr. Joseba Bikandi, University of the Basque Country)
  This tool is also similar to others available elsewhere. Only commercially available restriction enzymes have been included in the list, which has been obtained from REBASE. Minimum recognition size for restriction enzyme, type of endonuclease and additional options are customizable. It also provides a tool for restriction digest of two sequences to detect mutations
  http://www.in-silico.com/s_restriction/index.html
  Added: Thu Oct 30 2003, Hits: 7029, Reviews: 1 Read reviews  Write review   Cached
• WatCut (Michael Palmer, University of Waterloo)
  Watcut is an on-line tool and offers two basic functions (restriction analysis and silent mutation analysis) to help you with your cloning experiments. Restriction analysis works very much as usual. WatCut can display the results in a graphical format, as a plain table, or in a complete textual format along with the DNA and translated protein sequences. All of these displays can also be formatted for printing. Sequences may be supplied by file-upload or by copy-and-paste.
  Silent mutation analysis is intended for use with oligonucleotide sequences. It starts from a DNA (not protein) sequence, for which you also need to indicate the reading frame of protein translation. WatCut then scans your sequence for restriction sites that can be introduced without changing the encoded protein sequence. It will find sites created by any number of mutations, with both non-degenerate and degenerate recognition sequences - that is, it will find all possible sites. Provides printable output.
  http://watcut.uwaterloo.ca/watcut/watcut/template....
  Added: Mon Feb 17 2003, Hits: 2784, Reviews: 0  Write review   Cached