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FPGA
2004
ACM
163views FPGA» more  FPGA 2004»
14 years 1 months ago
Time and area efficient pattern matching on FPGAs
Pattern matching for network security and intrusion detection demands exceptionally high performance. Much work has been done in this field, and yet there is still significant roo...
Zachary K. Baker, Viktor K. Prasanna
CPM
2006
Springer
112views Combinatorics» more  CPM 2006»
14 years 1 months ago
Local Alignment of RNA Sequences with Arbitrary Scoring Schemes
Abstract. Local similarity is an important tool in comparative analysis of biological sequences, and is therefore well studied. In particular, the Smith-Waterman technique and its ...
Rolf Backofen, Danny Hermelin, Gad M. Landau, Oren...
USENIX
1994
13 years 11 months ago
TreadMarks: Distributed Shared Memory on Standard Workstations and Operating Systems
TreadMarks is a distributed shared memory DSM system for standard Unix systems such as SunOS and Ultrix. This paper presents a performance evaluation of TreadMarks running on Ultr...
Peter J. Keleher, Alan L. Cox, Sandhya Dwarkadas, ...
BMCBI
2007
233views more  BMCBI 2007»
13 years 10 months ago
160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA)
Background: To infer homology and subsequently gene function, the Smith-Waterman (SW) algorithm is used to find the optimal local alignment between two sequences. When searching s...
Isaac T. S. Li, Warren Shum, Kevin Truong
BMCBI
2008
115views more  BMCBI 2008»
13 years 10 months ago
PARPST: a PARallel algorithm to find peptide sequence tags
Background: Protein identification is one of the most challenging problems in proteomics. Tandem mass spectrometry provides an important tool to handle the protein identification ...
Sara Brunetti, Elena Lodi, Elisa Mori, Maria Stell...