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Parametric optimization of sequence alignment
Algorithmica, 1994zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Dan Gusfield +2 more
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Optimization of hindfoot alignment radiography
Acta Radiologica, 2016Background Cobey and Buck described methods to evaluate hindfoot alignment, but it is still unclear which method is better and easier to perform in clinical practice. Purpose To evaluate the optimal method for radiography of hindfoot ...
Chonglin, Yang +5 more
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Optimal Sequence Alignment to ED-Strings
2022Partial Order Alignment (POA) was introduced by Lee et al. in 2002 to allow the alignment of a string to a graph-like structure representing a set of aligned strings (a Multiple Sequence Alignment, MSA). However, the POA edit transcript (the sequence of edit operations that describe the alignment) does not reflect the possible elasticity of the MSA ...
Mwaniki, NM, Pisanti, N
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On Near-Optimal Alignments of Biological Sequences
Journal of Computational Biology, 1994A near-optimal alignment between a pair of sequences is an alignment whose score lies within the neighborhood of the optimal score. We present an efficient method for representing all alignments whose score is within any given delta from the optimal score.
Dalit Naor, Douglas L. Brutlag
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Alignment particle swarm optimization
2009 8th IEEE International Conference on Cognitive Informatics, 2009Particle swarm optimization (PSO) simulates the boids' collective behaviors. The original biological background of boid should follow three basic simple steering behaviors: separation, alignment and cohesion. However, to promote a fast convergent speed, the velocity update manner of each boid omits the alignment rule, this may result premature ...
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Consistency of optimal sequence alignments
Bulletin of Mathematical Biology, 1990Pairwise optimal alignments between three or more sequences are not necessarily consistent as a whole, but consistent and inconsistent residues are usually distributed in clusters. An efficient method has been developed for locating consistent regions when each pairwise alignment is given in the form of a "skeletal representation" (Bull. math. Biol. 52,
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Near-optimal sequence alignment
Current Opinion in Structural Biology, 1996Recent advances in algorithmic techniques and statistics of sequence alignment have helped to make near-optimal alignments an important tool in the delineation of biologically valid alignments. Near-optimal alignments serve to judge the reliability of portions of a sequence alignment.
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Pareto Optimal Pairwise Sequence Alignment
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2013Sequence alignment using evolutionary profiles is a commonly employed tool when investigating a protein. Many profile-profile scoring functions have been developed for use in such alignments, but there has not yet been a comprehensive study of Pareto optimal pairwise alignments for combining multiple such functions.
Kevin W. DeRonne, George Karypis
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Optimization of multiple‐sequence alignment based on multiple‐structure alignment
Proteins: Structure, Function, and Bioinformatics, 2005AbstractRoutinely used multiple‐sequence alignment methods use only sequence information. Consequently, they may produce inaccurate alignments. Multiple‐structure alignment methods, on the other hand, optimize structural alignment by ignoring sequence information.
Maxim, Shatsky +2 more
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Optimization of word alignment clues
Natural Language Engineering, 2005Statistical, linguistic, and heuristic clues can be used for the alignment of words and multi-word units in parallel texts. This article describes the clue alignment approach and the optimization of its parameters using a genetic algorithm. Word alignment clues can come from various sources such as statistical alignment models, co-occurrence tests ...
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