Abstract
Blast[2], FASTA[4] and related algorithms are popular tools for searching genomic data. Accelerating these tools is an increasingly important goal as the growth of the databases outstrips Moore’s Law[6]. Many of the existing hardware designs are little more than direct translations of existing algorithms from the software to hardware domain[3, 7]. In this paper we summarise a novel approach which we have implemented in VHDL and synthesised, with the aim of validating an efficient algorithm and virtual hardware search system which produces near perfect results compared to NCBI Blast 2.2.3. Speed and quality comparisons of the VHDL simulations with respect to NCBI Blast 2.2.3 are included.
Paul Gardner-Stephen: Author for correspondence.
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Gardner-Stephen, P., Knowles, G. (2003). A Novel Architecture for Genomic Sequence Searching and Alignment. In: Omondi, A., Sedukhin, S. (eds) Advances in Computer Systems Architecture. ACSAC 2003. Lecture Notes in Computer Science, vol 2823. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-39864-6_15
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DOI: https://doi.org/10.1007/978-3-540-39864-6_15
Publisher Name: Springer, Berlin, Heidelberg
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