OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics

OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics

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...

siDRM: an effective and generally applicable online siRNA design tool

Small interfering RNAs (siRNAs) have become an indispensable tool for the investigation of gene functions. Most existing siRNA design tools were trained on datasets assembled from confined origins, incompatible with the diverse siRNA laboratory practice to which these tools will ultimately be applied. We have performed an updated analysis using the disjunctive rule merging (DRM) approach on a l...

Efficient siRNA selection using hybridization thermodynamics

Small interfering RNA (siRNA) are widely used to infer gene function. Here, insights in the equilibrium of siRNA-target hybridization are used for selection of efficient siRNA. The accessibilities of siRNA and target mRNA for hybridization, as measured by folding free energy change, are shown to be significantly correlated with efficacy. For this study, a partition function calculation that con...

Thermodynamics of Microarray Hybridization

An Online Tool for Capstone Design Course Communication

The communication requirements associated with the instruction of a Capstone Design course can be extensive. This paper describes a utility used to simplify and improve communication between the instruction team members, and communication from the instruction team to the student design groups. This resource is part of a larger suite of tools that make use of a MySQL database to keep record of i...