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BMCBI
2007
247views more  BMCBI 2007»
13 years 7 months ago
A survey of DNA motif finding algorithms
Background: Unraveling the mechanisms that regulate gene expression is a major challenge in biology. An important task in this challenge is to identify regulatory elements, especi...
Modan K. Das, Ho-Kwok Dai
ALMOB
2008
131views more  ALMOB 2008»
13 years 7 months ago
Fast algorithms for computing sequence distances by exhaustive substring composition
The increasing throughput of sequencing raises growing needs for methods of sequence analysis and comparison on a genomic scale, notably, in connection with phylogenetic tree reco...
Alberto Apostolico, Olgert Denas
PPOPP
1999
ACM
13 years 12 months ago
Automatic Parallelization of Divide and Conquer Algorithms
Divide and conquer algorithms are a good match for modern parallel machines: they tend to have large amounts of inherent parallelism and they work well with caches and deep memory...
Radu Rugina, Martin C. Rinard
IPPS
2000
IEEE
14 years 2 days ago
Optimization of Motion Estimator for Run-Time-Reconfiguration Implementation
In this paper, we present a method to estimate the number of reconfiguration steps that a time-constrained algorithm can accommodate. This analysis demonstrates how one would attac...
Camel Tanougast, Yves Berviller, Serge Weber
IPPS
2002
IEEE
14 years 18 days ago
Parallel Out-of-Core Algorithm for Genome-Scale Enumeration of Metabolic Systemic Pathways
Systemic pathways-oriented approaches to analysis of metabolic networks are effective for small networks but are computationally infeasible for genome scale networks. Current comp...
Nagiza F. Samatova, Al Geist, George Ostrouchov, A...