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Firstly, while Circoletto aligns sequences using BLAST (local alignment) the alignment algorithm used in PGC is based on the NUCmer (global alignment) package in MUMmer, which is suitable for large-scale and rapid genome alignment.
Compared with Circoletto, which aligns desired sequences using BLAST (local alignment); the alignment algorithm used in PGC is based on the NUCmer (global alignment) package in MUMmer, which is more suitable for large-scale and rapid genome alignment (44, 48).
In strap-down gyro-compass in-motion alignment, the alignment accuracy depends not only on the quality of the gyroscopes and accelerometers, but also on the accuracy of the velocity provided by the aiding sensors such as odometers.
Graph alignment adopts concepts from sequence alignment; the alignment scores are adjusted to reflect topological or relational information for the graphs.
In addition to the standard scoring elements for pairwise alignment, the alignment of rearranging antigen receptors requires an additional scoring element for the treatment of N nucleotides.
To give the best alignment, the alignment parameter Constraint E-value and Word Size were adjusted for different datasets when using COBALT.
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Note that for spliced alignments the alignment strand has been changed to RNA-direction (as indicated by the dinucleotide-consensus) and alignments overlapping ribosomal RNA genes have been removed.
In the case of ambiguous alignments, the alignments with the highest total coverage and identity were kept (total 607).
In particular we are interested in the quality of what we deem the "transitive alignments," the alignments between the known elements on one genome and the newly found elements on the other genome.
Therefore, there are eight possible combinations of specificity for alignment A, alignment B or the consensus (Fig. 1B).
People who work at Patagonia are very much aligned with the values of the company, and I think that makes the organization extremely strong and effective because we have that alignment and the alignment is about a much more than just matching profits.
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