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Suppose the "true" alignment aligns only the first three symbols (i.e., AAA) of x and y, hence the last three symbols in the respective sequences are regarded as insertions that do not have any matching counterpart in the other sequence.
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.
The sum-of-pairs score (SPS) is the proportion of aligned pairs of nucleotides/amino-acids from the true alignment that are also aligned together in the test alignment.
S xy can be interpreted as a log likelihood ratio: where A x is the probability (abundance) of base x in the reference, B y is the probability of y in the query, M xy is the probability of x aligned to y in a true alignment and T is an arbitrary scale factor.
However, it is still possible to evaluate the relative accuracy by comparing the results from two aligners using the principle that the true alignment tends to have a considerably higher alignment score, because most errors arise from failing to find a seed.
We define a true alignment as a situation when a read is aligned back into the same position from which it was generated.
We consider the read to be aligned correctly if at least one of the nucleotides in the read is aligned to the same one in the genome as given by the true alignment.
Closing the eyes made "true" alignment easier.
Before reaching out for an Influencer, dig deeper to make sure that there is true alignment and you actually LIKE that person and would want to bring them home to meet your mom.
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Both scoring schemes were restricted to core blocks within the reference sequences where the 'true' alignment is known.
Leadership psychologist and coach Edgar Papke is the author of the book True Alignment.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com