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They are more than admirable in their concentration as they move in and out of classical alignment and into ballet's classroom positions.
He has always seemed a dancer of Apollonian purity, an impression borne out in the cover photograph by the perfect classical alignment of Mr. Baryshnikov in the air in the "Don Quixote" pas de deux.
In other words, N-maps computing acts over these positions like a classical alignment.
Naturally, as these two domains are shuffled between the two sequences, a classical alignment could not point out the two homologies at once.
A given classical alignment (which is also a map between positions) can be seen, for a certain positive integer N, as a N-map, both of s over t and of t over s.
When performed on a single organism, the Cildb BLAST output provides, in addition to classical alignment output, links to protein pages of Cildb as well as to BioMart views of target proteins, to be filtered by other criteria or displayed with Cildb attributes.
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Unlike classical alignments, the syntenic global alignment is composed of three types of blocks: highly conserved, conserved and unconserved blocks.
MEME (Bailey and Elkan, 1994) is an almost classical alignment-based motif discovery algorithm.
A set of experiments on simulated and real reads data confirms that the new measures are superior to other classical alignment-free statistics, especially when erroneous reads are considered.
On simulated DNA and protein sequences, the multiple-pattern approach led to results not much worse and sometimes even better than the classical alignment-based approach to phylogeny reconstruction.
Instead, evolutionary constraints also apply to binding effects, which depend on the spatial structure and accessibility of the DNA and on binding affinities (also weak binding) of transcription factor molecules to the DNA, which classical alignments based on sequence (Smith-Waterman, BLAST) fail to consider.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com