Processing Repetitive Sequence Structures at Streaming Rate with an FPGA ∗

Abstract

With the accelerating growth of biological databases and the beginning of genomescale processing, cost-effective high-performance sequence analysis remains an essential problem in bioinformatics. We examine the use of FPGAs for finding repetitive structures such as tandem repeats and palindromes under various mismatch models. For all problems addressed here… (More)

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