OligoWalk -- an online siRNA design tool utilizing hybridization thermodynamics
What you can do:
An online sever calculating thermodynamic features of sense-antisense hybridization.
Highlights:
- Given an mRNA sequence as input, the OligoWalk web server generates a list of small interfering RNA (siRNA) candidate sequences, ranked by the probability of being efficient siRNA (silencing efficacy greater than 70%).
- To accomplish this, the server predicts the free energy changes of the hybridization of an siRNA to a target mRNA, considering both siRNA and mRNA self-structure.
- The free energy changes of the structures are rigorously calculated using a partition function calculation.
- By changing advanced options, the free energy changes can also be calculated using less rigorous lowest free energy structure or suboptimal structure prediction methods for the purpose of comparison.
- Considering the predicted free energy changes and local siRNA sequence features, the server selects efficient siRNA with high accuracy using a support vector machine.
- On average, the fraction of efficient siRNAs selected by the server that will be efficient at silencing is 78.6%.
Keywords:
- siRNA design
- siRNA
- sense-antisense hybridization
- thermodynamic
- small interfering RNA
- silencing
Literature & Tutorials:
This record last updated: 07-21-2008