Joseph M. Lancaster

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Motivation: Large-scale DNA sequence comparison, as implemented by BLAST and related algorithms, is one of the pillars of modern genomic analysis. One way to accelerate these computations is with a streaming architecture, in which processors are arranged in a pipeline that replicates the multistage structure of the algorithm. To achieve high performance,(More)
Biosequence similarity search is an important application in modern molecular biology. Search algorithms aim to identify sets of sequences whose extensional similarity suggests a common evolutionary origin or function. The most widely used similarity search tool for biosequences is BLAST, a program designed to compare query sequences to a database. Here, we(More)
Large-scale protein sequence comparison is an important but compute-intensive task in molecular biology. The popular BLASTP software for this task has become a bottleneck for proteomic database search. One third of this software's time is spent executing the Smith-Waterman dynamic programming algorithm. This work describes a novel FPGA design for banded(More)
BLASTP is the most popular tool for comparative analysis of protein sequences. In recent years, an exponential increase in the size of protein sequence databases has required either exponentially more runtime or a cluster of machines to keep pace. To address this problem, we have designed and built a high-performance FPGA-accelerated version of BLASTP,(More)
Comparison between biosequences and probabilistic models is an increasingly important part of modern DNA and protein sequence analysis. The large and growing number of such models in today's databases demands computational approaches to searching these databases faster, while maintaining high sensitivity to biologically meaningful similarities. This work(More)
Large-scale protein sequence comparison is an important but compute-intensive task in molecular biology. BLASTP is the most popular tool for comparative analysis of protein sequences. In recent years, an exponential increase in the size of protein sequence databases has required either exponentially more running time or a cluster of machines to keep pace.(More)
Noise may play a pivotal role in gene circuit functionality, as demonstrated for the genetic switch in the bacterial phage lambda. Like the lambda switch, bacterial quorum sensing (QS) systems operate within a population and contain a bistable switching element, making it likely that noise plays a functional role in QS circuit operation. Therefore, a(More)
Embedded computing platforms have long incorporated non-traditional architectures (e.g., FPGAs, ASICs) to combat the diminishing returns of Moore’s Law as applied to traditional processors. These specialized architectures can offer higher performance potential in a smaller space, higher power efficiency, and competitive costs. A price is paid, however, in(More)
Hybrid computing systems (incorporating FPGAs, GPUs, etc.) have received considerable attention recently as an approach to significant performance gains in many problem domains. Deploying applications on these systems, however, has proven to be difficult and very labor intensive. In this paper we present our vision of the application development languages(More)
Desmethylimipramine (DMI) has been shown to interact with the N-methyl-D-aspartate (NMDA) receptor complex. Its probable action is through blockade of the cationic channel at the phencyclidine site and as a result it has potential anticonvulsant action. In this present study we have investigated the effects of DMI and ketamine on both NMDA-induced and(More)