TY - GEN
T1 - Biosequence similarity search on the Mercury system
AU - Krishnamurthy, Praveen
AU - Buhler, Jeremy
AU - Chamberlain, Roger
AU - Franklin, Mark
AU - Gyang, Kwame
AU - Lancaster, Joseph
PY - 2004
Y1 - 2004
N2 - Biosequence similarity search is an important application in modern molecular biology. Search algorithms aim to identify sets of sequences whose extensional similarity suggests a common evolutionary origin or function. The most widely used similarity search tool for biosequences is BLAST, a program designed to compare query sequences to a database. Here, we present the design of BLASTN, the version of BLAST that searches DNA sequences, on the Mercury system, an architecture that supports high-volume, high-throughput data movement off a data store and into reconfigurable hardware. An important component of application deployment on the Mercury system is the functional decomposition of the application onto both the reconfigurable hardware and the traditional processor. Both the Mercury BLASTN application design and its performance analysis are described.
AB - Biosequence similarity search is an important application in modern molecular biology. Search algorithms aim to identify sets of sequences whose extensional similarity suggests a common evolutionary origin or function. The most widely used similarity search tool for biosequences is BLAST, a program designed to compare query sequences to a database. Here, we present the design of BLASTN, the version of BLAST that searches DNA sequences, on the Mercury system, an architecture that supports high-volume, high-throughput data movement off a data store and into reconfigurable hardware. An important component of application deployment on the Mercury system is the functional decomposition of the application onto both the reconfigurable hardware and the traditional processor. Both the Mercury BLASTN application design and its performance analysis are described.
UR - http://www.scopus.com/inward/record.url?scp=11244355264&partnerID=8YFLogxK
U2 - 10.1109/ASAP.2004.1342485
DO - 10.1109/ASAP.2004.1342485
M3 - Conference contribution
AN - SCOPUS:11244355264
SN - 0769522262
T3 - Proceedings of the International Conference on Application-Specific Systems, Architectures and Processors
SP - 365
EP - 375
BT - Proceedings - 15th IEEE International Conference on Applications-Specific Systems, Architectures and Processors
T2 - Proceedings - 15th IEEE International Conference on Applications-Specific Systems, Architectures and Processors
Y2 - 27 September 2004 through 29 September 2004
ER -