In this paper we describe the parallelization of a dynamic programming algorithm used to find common RNA secondary structures including pseudoknots and similar structures. The se...
Many scientific applications manipulate large amount of data and, therefore, are parallelized on high-performance computing systems to take advantage of their computational power a...
Many applications of parallel I/O perform non-contiguous file accesses: instead of accessing a single (large) block of data in a file, a number of (smaller) blocks of data scatt...
In this paper, we describe a generalized approach to deriving a custom data layout in multiple memory banks for array-based computations, to facilitate high-bandwidth parallel mem...
We present a new bit-parallel technique for approximate string matching. We build on two previous techniques. The first one, BPM [Myers, J. of the ACM, 1999], searches for a patte...