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» Constraint Based Methods for Biological Sequence Analysis
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BMCBI
2006
139views more  BMCBI 2006»
15 years 18 days ago
Improvement in accuracy of multiple sequence alignment using novel group-to-group sequence alignment algorithm with piecewise li
Background: Multiple sequence alignment (MSA) is a useful tool in bioinformatics. Although many MSA algorithms have been developed, there is still room for improvement in accuracy...
Shinsuke Yamada, Osamu Gotoh, Hayato Yamana
107
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ICAPR
2005
Springer
15 years 6 months ago
Hierarchical Clustering of Dynamical Systems Based on Eigenvalue Constraints
Abstract. This paper addresses the clustering problem of hidden dynamical systems behind observed multivariate sequences by assuming an interval-based temporal structure in the seq...
Hiroaki Kawashima, Takashi Matsuyama
SIAMJO
2000
108views more  SIAMJO 2000»
15 years 10 days ago
Smooth SQP Methods for Mathematical Programs with Nonlinear Complementarity Constraints
Mathematical programs with nonlinear complementarity constraints are reformulated using better-posed but nonsmooth constraints. We introduce a class of functions, parameterized by...
Houyuan Jiang, Daniel Ralph
84
Voted
RECOMB
2008
Springer
16 years 26 days ago
CompostBin: A DNA Composition-Based Algorithm for Binning Environmental Shotgun Reads
A major hindrance to studies of microbial diversity has been that the vast majority of microbes cannot be cultured in the laboratory and thus are not amenable to traditional method...
Sourav Chatterji, Ichitaro Yamazaki, Zhaojun Bai, ...
97
Voted
BMCBI
2010
90views more  BMCBI 2010»
15 years 20 days ago
Local alignment of generalized k-base encoded DNA sequence
Background: DNA sequence comparison is a well-studied problem, in which two DNA sequences are compared using a weighted edit distance. Recent DNA sequencing technologies however o...
Nils Homer, Stanley F. Nelson, Barry Merriman