Result: Large scale protein sequence alignment using FPGA reprogrammable logic devices

Title:
Large scale protein sequence alignment using FPGA reprogrammable logic devices
Authors:
DYDEL, Stefan, BALA, Piotr
Source:
FPL 2004 : field-programmable logic and applications (Antwerp, 30 August - 1 September 2004)Lecture notes in computer science. :23-32
Publisher Information:
Berlin: Springer, 2004.
Publication Year:
2004
Physical Description:
print, 29 ref
Original Material:
INIST-CNRS
Subject Terms:
Computer science, Informatique, Mathematics, Mathématiques, Sciences exactes et technologie, Exact sciences and technology, Sciences appliquees, Applied sciences, Informatique; automatique theorique; systemes, Computer science; control theory; systems, Logiciel, Software, Traitement des langages et microprogrammation, Language processing and microprogramming, Electronique, Electronics, Electronique des semiconducteurs. Microélectronique. Optoélectronique. Dispositifs à l'état solide, Semiconductor electronics. Microelectronics. Optoelectronics. Solid state devices, Circuits intégrés, Integrated circuits, Circuits intégrés par fonction (dont mémoires et processeurs), Integrated circuits by function (including memories and processors), Alignement séquence, Sequence alignment, Alineación secuencia, Architecture reconfigurable, Reconfigurable architectures, Base donnée, Database, Base dato, Bioinformatique, Bioinformatics, Bioinformática, Circuit programmable, Programmable circuit, Circuito programable, Complexité calcul, Computational complexity, Complejidad computación, Conception circuit, Circuit design, Diseño circuito, DNA, Protéine, Protein, Proteína, Réseau porte programmable, Field programmable gate array, Red puerta programable, Réseau systolique, Systolic network, Red sistólica, Séquence aminoacide, Aminoacid sequence, Secuencia aminoácido
Document Type:
Conference Conference Paper
File Description:
text
Language:
English
Author Affiliations:
Faculty of Mathematics and Computer Science, N. Copernicus University, Chopina 12/8, 87-100 Torun, Poland
ISSN:
0302-9743
Access URL:
http://pascal-francis.inist.fr/vibad/index.php?action=search&terms=16107556
Rights:
Copyright 2004 INIST-CNRS
CC BY 4.0
Sauf mention contraire ci-dessus, le contenu de cette notice bibliographique peut être utilisé dans le cadre d’une licence CC BY 4.0 Inist-CNRS / Unless otherwise stated above, the content of this bibliographic record may be used under a CC BY 4.0 licence by Inist-CNRS / A menos que se haya señalado antes, el contenido de este registro bibliográfico puede ser utilizado al amparo de una licencia CC BY 4.0 Inist-CNRS
Notes:
Computer science; theoretical automation; systems

Electronics
Accession Number:
edscal.16107556
Database:
PASCAL Archive

Further Information

In this paper we show how to significantly accelerate Smith-Waterman protein sequence alignment algorithm using reprogrammable logic devices - FPGAs (Field Programmable Gate Array). Due to perfect sensitivity, the Smith-Waterman algorithm is important in a field of computational biology but computational complexity makes it impractical for large database searches when running on general purpose computers. Current approach allows for aminoacid sequence alignment with full substitution matrix which leads to more complex formula than used in DNA alignment and is much more memory demanding. We propose different parellization scheme than commonly used systolic arrays, leading to full utilization of PUs (Processing Units), regardless of sequence length. FPGA based implementation of Smith-Waterman algorithm can accelerate sequence alignment on a Pentium desktop computer by two orders of magnitude comparing to standard OSEARCH program from FASTA package.