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Description Edit

The NEBcutter is a database where a user can paste a DNA sequence they have obtained (via sequencing techniques) and see what, if any, restriction enzyme cut sites there are. NEBcutter is based off of the database called REBASE (Restriction Enzyme dataBASE) that is hosted by New England Biolab. They are a company that provides scientists with multiple different products for use in a lab environment i.e buffers, enzymes, etc. NEB also provides tools and resource programs for scientists to use free of charge.

Walk through of site Edit

NEBwebsite

1. Go to New England BioLabs website.

2. To the tab labelled "Tools and Resources".

3. Click the "NEBcutter"

NEBcutter

4. NEBcutter V2.0 will appear and paste your DNA sequence into the available space.

Note: There are other options here that can be checked and unchecked.

  • GenBank number- this refers to the NIH genetic sequence database. This number correlates to that specific sequence in that database for that specific organism.
NEB cutter 2
  • One must specify if the DNA is linear or circular. This would be helpful in the case of bacteria which have a circular plasmid.
  • Enzymes to use- this refers to the kind of restriction enzymes you want to be scanned for in your sequence of DNA. They can be specified to only the ones from NEB laboratory or different enzymes.
  • Standard sequences- this refers to the standard sequences that you can pick from this list.

Results Edit

(note: Used pACPm plasmid as an example)

Plasmid cut site

When the user enters his/her sequence into NEBcutter, this is what their results will look like. In this case since plasmid pACPm was used, its DNA is circular and is shown as such.

The figure to the right shows all the cut sites on that particular plasmid. It also indicates if the restriction enzyme can be purchased through New England Biolab or some other supplier.

Cut site

If the user clicks on a specific restriction enzyme, a new window pops up. This new window displays the name of the restriction enzyme and where it cuts exactly in the plasmid pACPm sequence. It has other information as well about where you can buy this restriction enzyme and what buffer would work well with this digestion.