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These were to close and demolish it, to refurbish it at an estimated cost of £1.6 million, and to build a new bridge on the same site but a different alignment, to eliminate the awkward turn at the west end, which was costed at £2 million.
This will cause a different alignment to be generated.
We examine this tradeoff and find that, because of a loss of information in the early steps of the approach, the alignments generated by the most common multiple sequence alignment programs are inherently unstable, and simply reversing the order of the sequences in the input file will cause a different alignment to be generated.
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From the scorecard, the user can select or deselect different alignments to be used in the EvoPrint analysis.
We propose a method based on majority voting across different alignments to (partially) account for these errors.
Even if the scoring system would be appropriate to identify the best alignment between the target and a single template this would not necessarily imply that the score can be used to compare and rank different alignments to different template structures or the resulting model structures.
This different way of treating the prealignment implies the need of different alignment strategies to delineate evolutionary conserved regions prior to the actual motif detection.
Six different partial charge calculation methods were used in combination with two different alignment methods to scrutinize their effects on the predictive power of 3D-QSAR models.
(c) Different alignment media, to access multiple independent sets of RDCs, can result in differential perturbations on the conformational freedom.
As described in Markova-Raina et al., not all alignment errors are created equal, and even PRANK, which was reported to outperform other aligners in simulation [ 46], still has a high false positives rate; therefore, one must compare the results of different alignment programs to reduce the rate of false positives in estimates of positive selection.
In the present study, the critical shear stress (CSS) for various Al/Si and Al/Al interfaces was determined using molecular dynamics and MEAM potential for different alignments (normal to the interface) and orientations (parallel to the interface).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com