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IVC
2007
102views more  IVC 2007»
13 years 7 months ago
Analysis of the rubberband algorithm
We consider simple cube-curves in the orthogonal 3D grid of cells. The union of all cells contained in such a curve (also called the tube of this curve) is a polyhedrally bounded s...
Fajie Li, Reinhard Klette
BMCBI
2005
93views more  BMCBI 2005»
13 years 7 months ago
Computing expectation values for RNA motifs using discrete convolutions
Background: Computational biologists use Expectation values (E-values) to estimate the number of solutions that can be expected by chance during a database scan. Here we focus on ...
André Lambert, Matthieu Legendre, Jean-Fred...
JASIS
2007
122views more  JASIS 2007»
13 years 7 months ago
Exploiting parallelism to support scalable hierarchical clustering
A distributed memory parallel version of the group average Hierarchical Agglomerative Clustering algorithm is proposed to enable scaling the document clustering problem to large c...
Rebecca Cathey, Eric C. Jensen, Steven M. Beitzel,...
BMCBI
2005
119views more  BMCBI 2005»
13 years 7 months ago
GASH: An improved algorithm for maximizing the number of equivalent residues between two protein structures
Background: We introduce GASH, a new, publicly accessible program for structural alignment and superposition. Alignments are scored by the Number of Equivalent Residues (NER), a q...
Daron M. Standley, Hiroyuki Toh, Haruki Nakamura
JCB
2007
97views more  JCB 2007»
13 years 7 months ago
Parsing Nucleic Acid Pseudoknotted Secondary Structure: Algorithm and Applications
Accurate prediction of pseudoknotted nucleic acid secondary structure is an important computational challenge. Prediction algorithms based on dynamic programming aim to find a st...
Baharak Rastegari, Anne Condon