This application allows the user
to determine where restriction enzymes will his/her sequence of interest. The
program used will map out all the sites where the specific restriction
endonuclease activity will occur on the sequence for a particular restriction
enzyme.
Instructions:
1. Type in the title for
the sequence (optional).
2. Select the “copy and
paste your sequence in the box” option.
3. Select, Copy (Ctrl + C) and Paste (Ctrl + V); or type your sequence in the box provided.
Select: Highlight your nucleotide sequence by clicking on the left mouse button, holding the button down while dragging the cursor over the region to be highlighted, then release mouse button.
Copy: Use command from the Edit box of the Explorer window or by pressing CTRL + C on the keyboard.
Paste: No specific format required. Use the Paste command from the Edit box of the Explorer window or press CTRL + V on the keyboard.
-OR- You may also upload a
sequence file from your computer or you can search for a sequence in the NCBI
data bank by entering a keyword.
4. Choose the type of analysis you wish the program to perform.
5. Select the type of output you wish the results to be displayed.
6. Select the enzymes
you wish to include in the display.
7. Select the restriction enzymes you wish to include in the analysis.
You can choose: All the enzymes in the database
Enzymes
with recognition site of a certain size
The enzymes from the list provided
in the box.
8. If you decide to select the enzymes individually, you can choose from the list provided by clicking on the name of the enzyme with the left mouse button.
To choose multiple enzymes, hold
down on the Shift or Control keypads on the keyboard while choosing with the
mouse button.
- Shift
key is used to choose successively.
- Control
key is used to choose randomly.
9. After you have selected your options, click on the “Analyze Sequence” button to run the program.
- Many restriction enzymes contain
ambiguous nucleotides in their sequence. To help you analyze the cut sites,
here is the recognition sequence nomenclature to represent ambiguity.
RECOGNITION SEQUENCE NOMENCLATURE:
REBASE Recognition sequences representations use the standard abbreviations
(Eur. J. Biochem. 150: 1-5, 1985) to represent ambiguity:
R = G or A
Y = C or T
M = A or C
K = G or T
S = G or C
W = A or T
B = not A
(C or G or T)
D = not C
(A or G or T)
H = not G
(A or C or T)
V = not T
(A or C or G)
N
= A or C or G or T
- The color or boldface highlights
represent the standard polylinker sequences and restriction enzymes that cut
those sequences.
- If you would like to learn more
about the restriction enzyme of interest, the hyperlink to a restriction enzyme
database may help.
New England
BioLabs' Official Restriction Enzyme DataBASE (REBASE Homepage)
When you are ready, click
here to start.