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The gel images were aligned by automated calculation of alignment vectors.
Then, by observing the dependencies, for the calculation of alignment score D in the current column (as indicated in green in Figure 2(c)), at most two preceding columns (as indicated in orange in Figure 2(c)) are needed.
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One calculation of alignments within around thirty degrees (about as close as they can get) shows that the last such alignment was in 561 BC, and the next will be in 2854.
Given a classification, it could then be used for the calculation of alignments.
Residues with the lowest correlations with respect to backcalculated data (11, 19, 20, 23, 35, 45, 46, 48 and 63) were excluded from the fit (and the calculation of the alignment tensor).
Calculation of an alignment with CLUSTALW software [ 33].
Thus, an ITS2 specific 12 × 12~scoring matrix was used for calculation of the alignment [ 73, 74].
Thus, an ITS2 specific 12 × 12 scoring matrix was used for calculation of the alignment [ 23].
At the gaps in the alignments, at least 10% of the members (or at least 2) had to have non-gap characters in the gap position to be included in the diversity calculation of the alignment.
The way proteins are assembled could influence the calculation of the alignment's coverage since the length of these sequences could differ from those experimentally solved (e.g. the presence of pre- and/or pro-domains in the annotated sequence).
In each BLAST run, the effective size of the generic database (i.e., NR, NT, etc). is specified using the -z flag to allow accurate calculation of the alignment E-value.
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