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For this, a kernel has been created for each feature and the alignment is calculated by the following expression: A_{v} ={ {sum_ k_{v}(i,j) cdot{yy^{t}(i,j }} over {sqrt{sum_ {{k_{v}^{2}}}left i,jright cdot{sum_{m=1}^{i}left(n{s_{m}^{2}}right)}}}} (3).
An alignment is calculated by measuring the azimuth, the angle from north, of the structure and the altitude of the horizon it faces The azimuth is usually measured using a theodolite or a compass.
A score for each column in the alignment is calculated using the concept of continuous sequence space introduced by Vingron and Sibbald [64] and the column scores are then summed over the full length of the alignment.
The optimal structure element alignment is calculated using dynamic programming.
bThe total score of an alignment is calculated as the sum of substitution and gap scores.
The variability in each column of the multiple sequence alignment is calculated using the Shannon entropy (H) function.
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Structural alignment was calculated using TM-align program [ 29] as implemented in T-Coffee package [ 30].
The % alignment was calculated as the percentage of reads that aligned to the hg18 human reference genome.
For quantitative characterization of the anisotropy and its decrease, the degree of alignment was calculated from the azimuthal scattering curves.
Main fibre diameter and orientation, as well as the degree of fibre alignment, were calculated, while a subset of the spun scaffolds were tested for their tensile properties.
Sequence alignment was calculated by smith-waterman alignment [43], while structure alignment was calculated by using jFATCAT [44].
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