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DTW constructs a global cost matrix by aligning the two temporal series.
The spectra exported from DataAnalysis were aligned through in-house software; the data were stored in a matrix by aligning all the peaks within an error of 1 ppm.
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Briefly, for each predicted seed motif, RCADE identifies the sequences with the largest motif scores, and constructs a new Position Weight Matrix (PWM) by aligning the motif hits in these sequences, repeating this procedure until the PWM converges.
Two p w i i matrices were obtained by aligning all 3' and 5' splice sites respectively, and by computing how frequently base w i appears at position i. 5' (donor) splices sites are defined as containing 3 exonic and 7 intronic bases, while 3' (acceptor) splice sites contain 3 exonic and 26 intronic bases [ 64, 66].
We prepared a matrix for phylogenetic analysis by aligning plastome sequences in MAFFT v. 6.864b.
We prepared a second matrix for phylogenetic analysis by aligning the sequences of rpoC2 from the plastomes of each species, the informatically assembled ψrpoC2 sequence from each species, and an outgroup plastid rpoC2 sequence from Nerium oleander (GenBank: GQ997692.1), a member of Apocynoideae (another subfamily of Apocynaceae), using MAFFT.
The multiphasic tissue-engineering construct is built by aligning the bone matrix with the capillary-like networks to enable the short-term culture and expansion of CD34+ cells.
Therefore, the 3D model of an object can be reconstructed by aligning those point clouds with the optimal transformation matrix.
The similarity of residue positions in the two structures is measured by aligning the contacts of the respective positions and by scoring the aligned neighbors via a substitution matrix (e.g. the Dayhoff matrix).
The amino acid sequences of this matrix were aligned by ClustalW with default options [ 45] and the resulting alignments were then used to guide the alignments of nucleotide coding sequences (CDSs).
It is assumed that the metamaterial is represented by aligned silver nanowires embedded into a semiconductor matrix, made of either silicon or gallium phosphide.
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