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In both cases, the alignment to the other complex TM segment were absent, hence these hits remained as false-positive cases.
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In both cases, the soft-clipped local alignment represents the "true" alignment, but the aligner has no way of knowing the location of the SV breakpoint, and thus will instead force a mismatched global alignment or leave the read unmapped.
In both cases the symmetry axis of the alignment is along the polarization vector, e, of the exciting light.
In both cases the E value for alignment with See2 is better than 1e-13 and for the C13 peptidase superfamily conserved domain E scores were of the order of 1e-80.
In some cases, the alignment between novel and previously described miRNAs extends well beyond the seed sequences, suggesting a common evolutionary ancestry.
In some cases the alignment contained only two sequences as the third sequence was absent or was considerably diverged from canonical KAP-β sequence.
For those cases, the alignment between the different pathways would have to be done by hand.
In almost all cases, the Alignment Score and BALiBASE score showed the same level of uncorrelation.
In two cases, the alignment to an A. thaliana CDS suggests that the probe lies within the coding region.
On the other hand, in many cases the alignment between the target and an appropriate template is good enough to build a good model, but the alignment method ranks this alignment lower than an alignment with a wrong template.
And in both cases, the exodus was encouraged by an alignment of exceptionally conducive political and economic circumstances: disgust with Labour and economic malaise in 1979; disgust with the Tories and an economy strong enough to entrust to Labour in 1997.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com