Fast Algorithms for Selecting Specific siRNA in Complete mRNA Data

Abstract. The Specific Selection Problem arises from the need to design short interfering RNA (siRNA) that aims at gene silencing. These short sequences target specific messenger RNA (mRNA) and cause the degradation of such mRNA, inhibiting the synthesis of the protein generated by it. In [11] this problem was solved in a reasonable amount of time when restricted to the design of siRNA for a particular mRNA, but their approach becomes too time consuming when trying to design siRNA for each mRNA in a given organism. We devise simple algorithms based on sorting and hashing techniques that allow us to solve this problem for the entire mRNA of the Human in less than 4 hours, obtaining a speedup of almost two orders of magnitude over previous approaches.