A parallel algorithm for predicting the secondary structure of polycistronic microRNAs

MicroRNAs (miRNAs) are newly discovered endogenous small non-coding RNAs (21-25nt) that target their complementary gene transcripts for degradation or translational repression. The biogenesis of a functional miRNA is largely dependent on the secondary structure of the miRNA precursor (pre-miRNA). Recently, it has been shown that miRNAs are present in the genome as the form of polycistronic transcriptional units in plants and animals. It will be important to design methods to predict such structures for miRNA discovery and its applications in gene silencing. In this paper, we propose a parallel algorithm based on the master-slave architecture to predict the secondary structure from an input sequence. First, the master processor partitions the input sequence into subsequences and distributes them to the slave processors. The slave processors will then predict the secondary structure based on their individual task. Afterward, the slave processors will return their results to the master processor. Finally, the master processor will merge the partial structures from the slave processors into a whole candidate secondary structure. The optimal structure is obtained by sorting the candidate structures according to their scores. Our experimental results indicate that the actual speed-ups match the trend of theoretic values.