Sentence examples for identity alignment from inspiring English sources
To aid in evaluating the networks, we create quartile plots of alignment percent identity, alignment length, and edge count versus edges binned by associated E-value (see Fig. S7).
Even more than in 4A, the most distant alignments in 4B are expected to have errors; in particular, the single edge between the Class A and Class C sequences in 4B, representing a 22% identity alignment over 135 amino acids, potentially represents a specious connection that should be undetectable from sequence information alone.
Especially, when candidate and reference sequences share a lower fractional identity, alignment accuracy drops significantly.
Figure 4B shows two extreme examples, a deep matrix (VT120) correcting a high identity alignment (dash-dot line) and a shallow matrix (VT40) correcting a low identity alignment (rounded-dash line).
As before, the word represents a stretch of total conservation in an otherwise low identity alignment (Fig. 6).
But this is not always the case; sometimes a high identity alignment is corrected by a distant matrix (dash-dot line) and vice versa (rounded-dash line).
Although we understand why high identity alignments might overextend when aligned with low target identity scoring matrices like BLOSUM62, matrix/target identity mismatch only accounts for about half of the overextensions we observed.
'Deeper' scoring matrices (scoring matrices targeted to more evolutionary change) produce longer less identical alignments by chance, whereas 'shallower' scoring matrices produce shorter higher identity alignments (Fig. 3).
Unfortunately, we cannot predict which lower identity alignments will overextend.
In contrast, incomplete alignment boundaries are more common in low identity alignments, whereas overextended alignment boundaries are more common in high identity alignments.
Gap penalties also modify alignment length and identity; increased gap penalties produce shorter higher identity alignments, whereas lower gap penalties produce longer lower identity alignments (Fig. 3).
