NP-Sticky: Model-Guided Ligation Calculator

Sticky End Finder

The sticky end finder is designed to find the optimal sticky ends from existing sequences. Sticky ends are ranked based on the discrimination between correct and misannealed free energies of ligation. A higher score indicates fewer misannealed structures.

In both examples above, the sticky end overhang is TCCA. The sticky end finder is most accurate between sticky ends with the same number of overhang bases. One application of the sticky end finder is to identify or create the best cloning sites in a display vector.

Please input DNA sequence (5'→3' upper strand) into the box below.


Number of overhang bases of sticky end:
5' overhang 3' overhang

Optional: Please input second DNA sequence (5'→3' upper strand) into the box below.


Number of overhang bases of sticky end:
5' overhang 3' overhang

Custom stacking energy
(Stacking energy is the stabilizing interaction between adjacent base pairs that forms when the nicks between DNA fragments are repaired. The default is from Forián et al. J Phys Chem B, 103, 884-892 (1999); alternately, you can choose stacking energy from Protozanova et al. J Mol Biol, 342, 775-785 (2004).)

Optional: Custom free energy for the repair of phosphodiester bonds (default is -6.3 kcal/mol)
 kcal/mol

Output display

Creative Commons License This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
The Python source code is available here: se_finder.cgi

Last modified by Daphne Ng on Jan 14th, 2014