Parallel out-of-core RNA pseudoknot prediction algorithm
MetadataShow full item record
RNA psuedoknot prediction is an algorithm for RNA sequence search and alignment. The difficulties of extending the RNA pseudoknot prediction algorithm to a parallel program are (1) it has complicated data dependences and (2) it has a large data set that typically cannot fit completely in main memory. In this paper we propose a new out-of-core parallel algorithm for RNA Pseudoknot prediction. Its novelty lies in its unique matrix partition ¡°piggybacking" communication and redundant file scheme. Experimental results obtained on 16 Sun UltraSPARC IIIi nodes provide evidence that our approach achieves good speedup. We found that counterintuitively the size of the in memory buffer is critical to efficiency of the parallel program.