The ability to rapidly identify a given protein from small subsamples (i.e. peptides) is at the basis of fundamental applications in the medical field. At the basis of protein identification we have a string matching problem which is computational intensive if we consider that the complexity of the algorithm scales with the length of the string and the number of sweeps of the database that are needed. In this paper we present an improvement for the FPGA-based string matching solution available in the literature improving the amount of parallelism exploited by the solution achieving a 1.63× reduction of the energy needed for the task over the literature and a 5.75× reduction when compared with high-end workstation.

Parallel protein identification using an FPGA-based solution

DURELLI, GIANLUCA CARLO;SANTAMBROGIO, MARCO DOMENICO
2016

Abstract

The ability to rapidly identify a given protein from small subsamples (i.e. peptides) is at the basis of fundamental applications in the medical field. At the basis of protein identification we have a string matching problem which is computational intensive if we consider that the complexity of the algorithm scales with the length of the string and the number of sweeps of the database that are needed. In this paper we present an improvement for the FPGA-based string matching solution available in the literature improving the amount of parallelism exploited by the solution achieving a 1.63× reduction of the energy needed for the task over the literature and a 5.75× reduction when compared with high-end workstation.
Proceedings - IEEE 28th International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2014
9781509021406
9781509021406
Computational Theory and Mathematics; Computer Networks and Communications; Hardware and Architecture; Software
File in questo prodotto:
File Dimensione Formato  
07529882.pdf

Accesso riservato

: Publisher’s version
Dimensione 355.65 kB
Formato Adobe PDF
355.65 kB Adobe PDF   Visualizza/Apri

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11311/1006278
Citazioni
  • ???jsp.display-item.citation.pmc??? ND
  • Scopus 1
  • ???jsp.display-item.citation.isi??? 1
social impact