Predicting the efficacy of short oligonucleotides in antisense and RNAi experiments with boosted genetic programming

Both small interfering RNAs (siRNAs) and antisense oligonucleotides can selectively block gene expression. Although the two methods rely on different cellular mechanisms, these methods share the common property that not all oligonucleotides (oligos) are equally effective. That is, if mRNA target sites are picked at random, many of the antisense or siRNA oligos will not be effective. Algorithms that can reliably predict the efficacy of candidate oligos can greatly reduce the cost of knockdown experiments, but previous attempts to predict the efficacy of antisense oligos have had limited success. Machine learning has not previously been used to predict siRNA efficacy.