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Development of technologies in bioinformatics resulted into many folds growth of biological data that led to the research for accelerated solutions in various domains of computational bioinformatics. String matching is one of the most widely performed tasks at various stages of computational pipeline and it needs an accelerated and reconfigurable methodology for implementation. In this paper we present...
This paper introduces an FPGA-based scheme to accelerate mpiBLAST, which is a parallel sequence alignment algorithm for computational biology. Recent rapidly growing biological databases for sequence alignment require high-throughput storage and network rather than computing speed. Our scheme utilizes a specialized hardware configured on an FPGA-board which connects flash storage and other FPGA-boards...
In this paper we propose an on-the-fly reconfigurable hardware-software codesign based reconfigurable solution for real-time protein identification. Reconfigurable string matching is performed in the disciplines of protein identification and biomarkers discovery. With the generation of plethora of sequenced data and number of biomarkers for several diseases, it is becoming necessary to have an accelerated...
The mapping of reads, i.e. short DNA base pair strings, to large genome databases has become a critical operation for genetic analysis and diagnosis. The underlying alignment operation essentially is a string search tolerating some character mismatches and possibly character deletions or insertions with respect to a reference genome. Its output comprises the locations within the reference that are...
BLAST[1] (Basic Local Alignment Search Tool) is a suite of programs used to identify similarity between genetic sequences. It is one of the most widely used tools in Bioinformatics. In recent years, with the size of gene and protein sequence database increasing exponentially, BLAST has become both a data-intensive and a computation-intensive application. How to run BLAST rapidly with low cost has...
With the growing numbers of both parallel architectures and related programming models, the benchmarking tasks become very tricky since parallel programming requires architecture-dependent compilers and languages as well as high programming expertise. More than just comparing architectures with synthetic benchmarks, benchmarking is also more and more used to design specialized systems composed of...
The current generation of genome sequencers produces orders of magnitude more sequencing data at a fraction of their former cost, a development that has repositioned the sequencing bottleneck from data acquisition to alignment and analysis. Optimal alignment algorithms, such as Smith-Waterman (SW), provide the most desirable output in terms of sensitivity and accuracy, but are perceived as too computationally...
Sequence alignment is an essential, but compute-intensive application in Bioinformatics. Hardware implementation speeds up this application by exploiting its inherent parallelism, where the performance of the hardware depends on its capability to align long sequences. In hardware terms, the length of a biological query sequence that can be aligned against a database sequence depends on the number...
In this paper, we present a novel method based on hardware partitioning to reduce the execution time and improve the resource utilization of biological sequence alignment, resulting in a higher performance as compared to conventional approaches. The paper shows that the method reduces the execution time and improves the resource utilization up to 33.3%. Further, equations are derived, showing the...
The cell BE is a heterogeneous multi-core processor offering multiple levels of parallelism. When these are properly leveraged, the cell BE demonstrates impressive performance acceleration for several high performance computing applications, including exact string matching on streaming data. The present study investigates the suitability of the cell BE for a string matching problem of relevance to...
BLASTn is a tool universally used by biologists to identify similarities between nucleotide based biological genome sequences. This report describes an hardware implementation designed to accelerate algorithm maintaining the same results yielded by the software developed at NCBI. A detailed profile study identifies the Blast_Nt_Scan function as the computationally intensive part of the algorithm....
Probably the single most important concern of the biotechnology industry is to improve existing biotechnology applications and tools due to the exponential increase in the size of the datasets. Improving application specific performance, pertaining to sudden and dynamic changes in the execution environment has been a widely researched problem. This research was undertaken to find application specific...
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