Memorias de investigación
Research Publications in journals:
FPGA Acceleration for DNA Sequence Alignment
Year:2007

Research Areas
  • Electronics engineering

Information
Abstract
In this paper, we present two new hardware architectures that implement the Smith¿ Waterman algorithm for DNA sequence alignment. Previous low-cost approaches based on Field Programmable Gate Array (FPGA) technology are reviewed in detail and then improved with the goal of increased performance at the same cost (i.e., area). This goal is achieved through low level optimizations aimed to adapt the systolic structure implementing the algorithm to the regular structure of FPGAs, essentially finding the optimum granularity of the systolic cells. The proposed architectures achieve processing rates close to 1 Gbps, clearly outperforming previous approaches. Comparing to the reported FPGA results of the computation of the edit-distance between two DNA sequences, throughput is doubled for the same clock frequency with a minimum area penalty. The design has been implemented on an FPGA-based prototyping board integrated into a bioinformatics system. This has allowed validating the approach in a real system (i.e., including I/O and database access), and comparing the proposed hardware solution to purely software approaches. As shown in the paper, the results are outstanding even for slow-rate buses.
International
Si
JCR
Si
Title
J CIRCUIT SYST COMP
ISBN
0218-1266
Impact factor JCR
0,13
Impact info
Volume
16
Journal number
2
From page
245
To page
266
Month
ABRIL
Ranking
Participants

Research Group, Departaments and Institutes related
  • Creador: Grupo de Investigación: Laboratorio de Sistemas Integrados (LSI)
  • Departamento: Ingeniería Electrónica