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LCTRTS
2010
Springer
13 years 6 months ago
Improving both the performance benefits and speed of optimization phase sequence searches
The issues of compiler optimization phase ordering and selection present important challenges to compiler developers in several domains, and in particular to the speed, code size,...
Prasad A. Kulkarni, Michael R. Jantz, David B. Wha...
BIBE
2008
IEEE
142views Bioinformatics» more  BIBE 2008»
14 years 3 months ago
Optimizing performance, cost, and sensitivity in pairwise sequence search on a cluster of PlayStations
— The Smith-Waterman algorithm is a dynamic programming method for determining optimal local alignments between nucleotide or protein sequences. However, it suffers from quadrati...
Ashwin M. Aji, Wu-chun Feng
PLDI
2012
ACM
11 years 11 months ago
Effective parallelization of loops in the presence of I/O operations
Software-based thread-level parallelization has been widely studied for exploiting data parallelism in purely computational loops to improve program performance on multiprocessors...
Min Feng, Rajiv Gupta, Iulian Neamtiu
ISMB
1994
13 years 10 months ago
An Improved System for Exon Recognition and Gene Modeling in Human DNA Sequence
A new version of the GRAIL system (Uberbacher and Mural, 1991; Mural et al., 1992; Uberbacher et al., 1993), called GRAILII, has recently been developed (Xu et al., 1994). GRAILII...
Yin Xu, J. Ralph Einstein, Richard J. Mural, Manes...
JCB
2007
130views more  JCB 2007»
13 years 8 months ago
Bayesian Inference of MicroRNA Targets from Sequence and Expression Data
MicroRNAs (miRNAs) regulate a large proportion of mammalian genes by hybridizing to targeted messenger RNAs (mRNAs) and down-regulating their translation into protein. Although mu...
Jim C. Huang, Quaid Morris, Brendan J. Frey