TY - JOUR
T1 - Biosequence similarity search on the mercury system
AU - Krishnamurthy, Praveen
AU - Buhler, Jeremy
AU - Chamberlain, Roger
AU - Franklin, Mark
AU - Gyang, Kwame
AU - Jacob, Arpith
AU - Lancaster, Joseph
N1 - Funding Information:
This work was supported by NSF Career grant DBI-0237902, NSF grants CNS-0313203, CCF-0427794 and CCR-0217334, and NIH/NGHRI grant 1 R42 HG003225-01 (the latter through BECS Technology, Inc.). R.D. Chamberlain is a principal in BECS Technology, Inc.
PY - 2007/10
Y1 - 2007/10
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.
KW - Biosequence
KW - Comparative annotation
KW - DNA sequencing
UR - https://www.scopus.com/pages/publications/35148876414
U2 - 10.1007/s11265-007-0087-0
DO - 10.1007/s11265-007-0087-0
M3 - Article
AN - SCOPUS:35148876414
SN - 1387-5485
VL - 49
SP - 101
EP - 121
JO - Journal of VLSI Signal Processing Systems for Signal, Image, and Video Technology
JF - Journal of VLSI Signal Processing Systems for Signal, Image, and Video Technology
IS - 1
ER -