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Most (73%) of the realigned incomplete alignment boundaries fall into the bin (orange).
A complete alignment indicates low divergence, whereas an incomplete alignment indicates substantial divergence.
Most incomplete alignment boundaries (73% for BLASTP, 76% for SSEARCH) were from alignments in the lowest two identity quartiles.
Restricting the analysis to the top 25 homologs further decreases incomplete alignment to 2%, whereas increasing overextension to 11%.
Reads exhibiting incomplete alignment, namely those with overlap percentages <90%, were called the RI sets (RI japonica, RI indica, RI nivara).
In contrast, incomplete alignment boundaries are more common in low identity alignments, whereas overextended alignment boundaries are more common in high identity alignments.
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Incomplete alignments that missed spacer regions due to deletions or genomic translocations were not used in our analysis.
Incomplete alignments are another example of inadequate alignment sensitivity.
Incomplete alignments had negative boundary errors and overextended alignments had positive boundary errors.
Their performance will have to be compared to other approaches to deal with incomplete alignments [ 14, 23].
The most overextended alignments (>40 residues, Fig. 2) decreased by 2217 alignment boundaries, whereas the most incomplete alignments increased by 399 boundaries.
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