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In this case, even efficient optimisation algorithms would lead to meaningless alignments.
It is possible that the underlying objective function is 'wrong' by assigning high numerical scores to biologically meaningless alignments.
This alone is enough evidence that a sequence alignment between these proteins is probably meaningless.
An alignment of a helix and a strand is meaningless in structural context as these regions, though equivalent in homologous proteins, do not share structural similarity.
The arithmetic of ordered set-valued functions is meaningless; hence, a novel concept, namely, generalized correlation, is proposed to handle shape alignment problems.
These scoring functions should be defined in such a way that biologically reasonable alignments or trees are more likely to receiving higher scores than biologically meaningless ones.
When genome similarities are calculated based on a global alignment of the opposite strands of two genomes, the result is just wrong and meaningless.
Meaningless twaddle?
"That aspect is meaningless.
Small, meaningless rebellion.
The world was meaningless.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com