PMID- 11928482
OWN - NLM
STAT- MEDLINE
DCOM- 20021001
LR  - 20130220
IS  - 2335-6928 (Print)
IS  - 2335-6928 (Linking)
DP  - 2002
TI  - High speed homology search with FPGAs.
PG  - 271-82
AB  - We will introduce a way how we can achieve high speed homology search by only 
      adding one off-the-shelf PCI board with one Field Programmable Gate Array (FPGA) 
      to a Pentium based computer system in use. FPGA is a reconfigurable device, and 
      any kind of circuits, such as pattern matching program, can be realized in a 
      moment. The performance is almost proportional to the size of FPGA which is used 
      in the system, and FPGAs are becoming larger and larger following Moore's law. We 
      can easily obtain latest/larger FPGAs in the form off-the-shelf PCI boards with 
      FPGAs, at low costs. The result which we obtained is as follows. The performance 
      is most comparable with small to middle class dedicated hardware systems when we 
      use a board with one of the latest FPGAs and the performance can be furthermore 
      accelerated by using more number of FPGA boards. The time for comparing a query 
      sequence of 2,048 elements with a database sequence of 64 million elements by the 
      Smith-Waterman algorithm is about 34 sec, which is about 330 times faster than a 
      desktop computer with a 1 GHz Pentium III. We can also accelerate the performance 
      of a laptop computer using a PC card with one smaller FPGA. The time for 
      comparing a query sequence (1,024) with the database sequence (64 million) is 
      about 185 sec, which is about 30 times faster than the desktop computer.
FAU - Yamaguchi, Yoshiki
AU  - Yamaguchi Y
AD  - Institute of Engineering Mechanics and Systems, University of Tsukuba, 1-1-1 
      Ten-ou-dai, Tsukuba, Ibaraki, 305-8573, Japan.
FAU - Maruyama, Tsutomu
AU  - Maruyama T
FAU - Konagaya, Akihiko
AU  - Konagaya A
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - United States
TA  - Pac Symp Biocomput
JT  - Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
JID - 9711271
SB  - IM
MH  - Computational Biology/methods
MH  - Oligonucleotide Array Sequence Analysis
MH  - *Sequence Homology, Nucleic Acid
MH  - *Software
MH  - Time Factors
EDAT- 2002/04/04 10:00
MHDA- 2002/10/03 04:00
CRDT- 2002/04/04 10:00
PHST- 2002/04/04 10:00 [pubmed]
PHST- 2002/10/03 04:00 [medline]
PHST- 2002/04/04 10:00 [entrez]
PST - ppublish
SO  - Pac Symp Biocomput. 2002:271-82.