We have verified that the subinteger feature of the proposed method provides us with extremely accurate range-bin alignments, in contrast to the minimum entropy-based approach.
This effect illustrates the advantage of clustering alignments in contrast to clustering the expression profiles directly.
The observation that 'deep' scoring matrices produce overextended alignments between domains that are less evolutionarily distant (have higher identity) than the scoring matrix target identity is not surprising, though the relationship between alignment boundaries (in contrast to internal alignment accuracy) and scoring matrices has not been extensively studied.
In contrast, alignment overextension occurs most often when closely related sequences are aligned, and thus becomes more frequent as sequence databases grow.
The backline was cramped, Mike Phillips too often running sideways before passing, and Wales's alignment behind was flat, in contrast to England who often brought in runners from deep when moving quick ball to attack space and generate width.
Alignment positions on CRM1, in contrast, showed very little constraint, suggesting a lack of nucleosome phasing.
In contrast, alignment of M. lucifugus sequence for IKZF1, LAMC3, SOX9, and SOX8 to other mammals is more conserved.
In contrast, alignment with ARPAnno gave the best score for ARP2 (29.1), but the score for ARP4 is just slightly lower (28.8), just as the score for actin (27.0).
In contrast, alignment of reads to the reference transcriptome results in 10% fewer correct assignments—only 13,250 of 15,027 total calls are correct and most incorrect assignments result in false positive eQTL.
