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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...
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...
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....
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