FPGA implementation of systolic sequence alignment

Hoang, D.T.; Lopresti, Daniel

doi:10.1007/3-540-57091-8_43

Cited by 41 publications

(16 citation statements)

References 4 publications

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“…The resultant hardware was a linear systolic array whose processing elements could differentiate between the alphabet and scores as perform comparison and addition operations. Newer architectures [21,22] have built upon this Lipton and Lopresti work by adding markers in processing elements to trace back optimal similarity paths.…”

Section: Sequence Alignment Architecturesmentioning

confidence: 99%

Race Logic: A hardware acceleration for dynamic programming algorithms

Madhavan

Sherwood

Strukov

2014

2014 ACM/IEEE 41st International Symposium on Computer Architecture (ISCA)

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Section: Sequence Alignment Architecturesmentioning

confidence: 99%

Race Logic: A hardware acceleration for dynamic programming algorithms

Madhavan

Sherwood

Strukov

2014

2014 ACM/IEEE 41st International Symposium on Computer Architecture (ISCA)

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“…In terms of the AM matrix, this means that the anti-diagonal values can be calculated concurrently, see Figure 2c. This property is effectively used for algorithm acceleration using dedicated hardware (Hoang and Lopresti, 1992) (Lavenier, 1998) (Yu et al, 2003) (Court and Herbordt, 2004). Typical hardware architecture is based on a systolic array of Processing Elements (PE) (see Figure 2c).…”

Section: Needleman-wunsch Hardware Accel-erationmentioning

confidence: 99%

Genomic PCR Simulation With Hardware-Accelerated Approximate Sequence Matching

Lexa¹,

Martínek²,

Beck³

et al. 2007

ECMS 2007 Proceedings Edited By: I. Zelinka, Z. Oplatkova, A. Orsoni

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We report the latest details on improvements made or planned for the VPCR simulation software currently accessible on the Internet (installed on servers in Padova and Brno). We describe the inner workings of the dynamic amplification simulation model, concentrating mostly on the time-and sensitivity-critical step of sequence matching. Replacement of BLAST by the more sensitive and faster PRIMEX similarity search program resulted in a marked improvement of PCR product predictions. Further speed improvements were acheived using hardware acceleration of approximate sequence matching. We report our theorethical computation time estimates and results of the first tests using the Arabidopis and human genome sequences as PCR templates.

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“…al. [2], [3] implemented the Needleman-Wunsch and dynamic programming algorithms using systolic array implementation on SPLASH 2 in order to achieve orders of magnitude higher performance than the conventional computers of that time. Using JBits S. Guccione et.…”

Section: Hardware Efforts For Sequence Comparisonmentioning

confidence: 99%

“…For that reason, the acceleration of BLAST through custom hardware architectures seems an appropriate first step in the speedup of DNA sequence comparison, and this is the purpose of this work. Historically, DNA string matching is one of the first applications of reconfigurable computing [2,3].…”

Section: Introductionmentioning

confidence: 99%