Treffer: Three-dimensional dynamic programming for homology search

Title:
Three-dimensional dynamic programming for homology search
Authors:
YAMAGUCHI, Yoshiki, MARUYAMA, Tsutomu, KONAGAYA, Akihiko
Source:
FPL 2004 : field-programmable logic and applications (Antwerp, 30 August - 1 September 2004)Lecture notes in computer science. :505-515
Publisher Information:
Berlin: Springer, 2004.
Publication Year:
2004
Physical Description:
print, 16 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, Calculateur embarqué, Boarded computer, Calculador embarque, Conception circuit, Circuit design, Diseño circuito, Elément matriciel, Matrix element, Elemento matricial, Haute performance, High performance, Alto rendimiento, Homologie, Homology, Homología, Modèle 2 dimensions, Two dimensional model, Modelo 2 dimensiones, Modèle 3 dimensions, Three dimensional model, Modelo 3 dimensiones, Ordinateur hôte, Host computer, Computador huesped, Parallélisme, Parallelism, Paralelismo, Programmation dynamique, Dynamic programming, Programación dinámica, Réseau porte programmable, Field programmable gate array, Red puerta programable, Serveur documentaire, Documentary server, Servidor documental
Document Type:
Konferenz Conference Paper
File Description:
text
Language:
English
Author Affiliations:
RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho Tsurumi-ku Yokohama Kanagawa, 230-0045, Japan
Institute of Engineering Systems and Mechanics, University of Tsukuba, 1-1-1 Ten-ou-dai Tsukuba Ibaraki, 305-8573, Japan
ISSN:
0302-9743
Access URL:
http://pascal-francis.inist.fr/vibad/index.php?action=search&terms=16107464
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.16107464
Database:
PASCAL Archive

Weitere Informationen

Alignment problems in computational biology have been focused recently because of the rapid growth of sequence databases. Many systems for alignment have been proposed to date, but most of them are designed for two-dimensional alignment (alignment between two sequences), because huge amount of memory and very long computational time are required by alignment among three or more sequences. In this paper, we describe a compact system with an off-the-shelf FPGA board and a host computer for three-dimensional alignment using Dynamic Programming. Through our approach, high performance are attained by two phase search with reconfigurations of an FPGA and co-processing the FPGA and software. Furthermore, in order to achieve higher parallelism in the FPGA, we use a payoff matrix for matching elements in sequences and the matrix is divided into sub-matrices which are minimized. In comparison to a single Intel Pentium4 2.53GHz processor, our system with a single XC2V6000 enables more than 250-fold speedup.