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It relies on the subroutines Align, which returns the best alignment between two series based on a given set of genes, and ScoreGene, which returns the score of two series when aligned using a given alignment and a specified gene.
In this paper, we address the challenging task of finding the best alignment between two 3D objects by solving a global optimization problem in the space of rotations SO(3).
This algorithm finds the best alignment between two strings and inserts a penalty if an error occurs (insertion, deletion and substitution), but no penalty is applied if the labels match.
To adjust for this, the UCSC conservation track, which is the best alignment between two genomes, is used instead.
The best alignment between two trajectories, p and q, is computed by minimizing the sum of the squared difference between all overlapping points: { T b e s t, τ b e s t } = arg min T, τ (∑ i w i ((q i + τ x − (T p i ) x ) 2 + (q i + τ y − (T p i ) y ) 2 ) ∑ i w i ), with w i = q i + τ f p i f.
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The dynamic time warping (DTW) method uses a dynamic programming technique for defining the best alignment between the two time series data Keogh and Ratanamahatana (2004).
Note that because the algorithm finds the best alignment between the two sequences, small inaccuracies in the input transcription will not reduce the quality of the final animation.
NETAL constructs an alignment score matrix and uses a broad search to find the best alignment between networks.
The Smith Waterman algorithm, an exact method, aims to find the best local alignment between two sequences.
The problem of inferring homologies between distantly related proteins, whose divergence is the result of frameshifts and point mutations, is approached in this paper by determining the best pairwise alignment between two DNA sequences that encode the proteins.
This additional path theoretically allows for the opening of a new gap within a gap, something which is automatically excluded if looking for the shortest path or best-scoring alignment between two sequences.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com