title: 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 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%. The OligoWalk web server is freely accessible through internet at http://rna.urmc.rochester.edu/servers/oligowalk.
authors.affiliation: Department of Biochemistry and Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, NY 14642, USA.
authors.forename: Zhi John
authors.initials: ZJ
authors.lastname: Lu
authors.forename: David H
authors.initials: DH
authors.lastname: Mathews
mesh_terms: D020407:Internet; D009693:Nucleic Acid Hybridization; D009841:Oligonucleotides / Q000737:chemistry; D034622:RNA Interference; D012333:RNA, Messenger / Q000737:chemistry; D034741:RNA, Small Interfering / Q000737:chemistry*; D017423:Sequence Analysis, RNA; D012984:Software; D013816:Thermodynamics; D014584:User-Computer Interface
chemical_list: D009841:Oligonucleotides; D012333:RNA, Messenger; D034741:RNA, Small Interfering