MOTIVATION Optimal sequence alignment based on the Smith-Waterman algorithm is usually too computationally demanding to be practical for searching large sequence databases. Heuristic programs like FASTA and BLAST have been developed which run much faster, but at the expense of sensitivity. RESULTS In an effort to approximate the sensitivity of an optimal alignment algorithm, a new algorithm h...

In this paper, we describe fully parallelized architectures for one-to-one, one-to-many, and many-to-many sequence alignments using Smith-Waterman algorithm. The architectures utilize the principles of parallelism and pipelining to the greatest extent in order to take advantage of both intrasequence and inter-sequence parallelization and to achieve high speed and throughput. First, we describe ...

Volunteer distributed computations utilize spare processor cycles of personal computers that are connected to the Internet. The resulting platforms provide computational power previously available only through the use of expensive clusters or supercomputers. However, distributed computations running in untrustworthy environments raise a number of security concerns, including computation integri...

—Whole genome comparison consists of comparing or aligning two genome sequences in the hope that analogous functional or physical characteristics may be observed. Sequence comparison is done via a number of slow rigorous algorithms, or faster heuristic approaches. However, due to the large size of genomic sequences, the capacity of current software is limited. In this work, we design a parallel...

Metabolic alterations including increased glycolysis are a common feature of many cancers. In their recent study, Lowengrub, Waterman, and colleagues (Lee et al, 2017) report a spatial pattern of glycolysis in solid tumors that occurs within the tumor microenvironment. This spatial organization is linked to gradients derived from Wnt signaling and nutrient availability that mediate a reaction-d...