Observatorio de I+D+i UPM

Memorias de investigación
Artículos en revistas:
FPGA Acceleration for DNA Sequence Alignment
Año:2007
Áreas de investigación
  • Industria electrónica
Datos
Descripción
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.
Internacional
Si
JCR del ISI
Si
Título de la revista
J CIRCUIT SYST COMP
ISSN
0218-1266
Factor de impacto JCR
0,13
Información de impacto
Volumen
16
DOI
Número de revista
2
Desde la página
245
Hasta la página
266
Mes
ABRIL
Ranking
Esta actividad pertenece a memorias de investigación
Participantes
  • Autor: C. Pedreira (Department of Engineering, University of Leicester (UK))
  • Autor: Gabriel Caffarena Fernandez (UPM)
  • Autor: Carlos Carreras Vaquer (UPM)
  • Autor: Octavio Nieto-Taladriz Garcia (UPM)
  • Autor: Slobodan Bojanic Antonijevic (UPM)
Grupos de investigación, Departamentos, Centros e Institutos de I+D+i relacionados
  • Creador: Grupo de Investigación: Laboratorio de Sistemas Integrados (LSI)
  • Departamento: Ingeniería Electrónica
S2i 2021 Observatorio de investigación @ UPM con la colaboración del Consejo Social UPM
Cofinanciación del MINECO en el marco del Programa INNCIDE 2011 (OTR-2011-0236)
Cofinanciación del MINECO en el marco del Programa INNPACTO (IPT-020000-2010-22)