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It was a case of perfect alignment.
The traditional Needleman-Wunsch algorithm [ 2] and its variants can be easily formulated as a special case of alignment with PHMMs (we call this approach Viterbi decoding).
It provides good convergence rates for first-order upwind discretisations even in the case of alignment, the flow being aligned with the grid.
The CPT measurements in case of alignment errors were highly reproducible between the two RCs with a κ value of 0.70 and an ICC of 0.92.
The distribution and density of the electromagnetic flux, and variation of efficiency versus load level of the system and responses of the system in case of different alignment errors are also investigated and reported for both ideal operation conditions and in case of alignment errors.
Despite the different methods and objectives for each classification, the high correspondence among the longleaf pine classes in each provided one notable case of alignment among the classifications.
These concepts are used by analogy with the case of alignment.
As this method, our approach is an attempt to avoid the introduction of some arbitrary costs on the transformations between sequences (like gap penalties in the case of alignment).
The averaging of signal across multiple regions of the same functional type facilitates the reduction of genome-wide results to summary statistics, but is complicated by the presence of missing data, e.g. missing CpGs in the case of methylation or indels in the case of alignment.
It was a case of club and player in perfect alignment.
In case of alignment-free discovery, the conservation of a motif is scored irrespective of its orientation or position within a promoter sequence.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com