OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics.

ABSTRACT: 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

SUBMITTER: Lu ZJ 

PROVIDER: S-EPMC2447759 | biostudies-literature | 2008 Jul

REPOSITORIES: biostudies-literature