How do I use the Agarose Gel tool to check the orientation of a ligated fragment.

The Agarose Gel tool allows you to quickly and easily create simulated agarose gels of your sequences cut with any combination of restriction enzymes. You can use this feature to identify site(s) that will generate unique patterns to differentiate successful clones, or to determine if fragments are sufficiently different in size to separate under particular gel conditions.

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1. Using the Cloning Clipboard subclone your digested fragment into your cloning vector
2. Save as "forward.nucl".
3. Now hold down SHIFT and repeat the subcloning.
4. Save as "reverse.nucl"
5. FILE | NEW | AGAROSE GEL
6. Drag a RE site from "forward.nucl" to the Agarose gel
7. Drag the same site from "reverse.nucl" to the Agarose gel

See the Simulated Agarose Gel help topic for more details.

Related Topics.

Simulated Agarose Gel

Restriction enzyme

Automatic Restriction Enzyme Analysis

Searching for restriction sites

Editing enzyme files

Click Cloning

Cloning Clipboard