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RIVF
2008
13 years 10 months ago
Speeding up subset seed algorithm for intensive protein sequence comparison
Abstract--Sequence similarity search is a common and repeated task in molecular biology. The rapid growth of genomic databases leads to the need of speeding up the treatment of thi...
Van Hoa Nguyen, Dominique Lavenier
ALMOB
2008
95views more  ALMOB 2008»
13 years 9 months ago
A stitch in time: Efficient computation of genomic DNA melting bubbles
Background: It is of biological interest to make genome-wide predictions of the locations of DNA melting bubbles using statistical mechanics models. Computationally, this poses th...
Eivind Tøstesen
JCB
2000
129views more  JCB 2000»
13 years 8 months ago
Prediction of RNA Base Pairing Probabilities on Massively Parallel Computers
We present an implementation of McCaskill's algorithm for computing the base pair probabilities of an RNA molecule for massively parallel message passing architectures. The p...
Martin Fekete, Ivo L. Hofacker, Peter F. Stadler
IPPS
2007
IEEE
14 years 3 months ago
Self Adaptive Application Level Fault Tolerance for Parallel and Distributed Computing
Most application level fault tolerance schemes in literature are non-adaptive in the sense that the fault tolerance schemes incorporated in applications are usually designed witho...
Zizhong Chen, Ming Yang, Guillermo A. Francia III,...
IPPS
1998
IEEE
14 years 1 months ago
Eliminating the Protocol Stack for Socket Based Communication in Shared Memory Interconnects
We show how the traditional protocol stack, such as TCP/IP, can be eliminated for socket based high speed communication within a cluster. The SCI shared memory interconnect is used...
Stein Jørgen Ryan, Haakon Bryhni