Similarly, in case of alignments to Su(HW) peaks, the region ranged halfway to the next peak.
In case of alignment-free discovery, the conservation of a motif is scored irrespective of its orientation or position within a promoter sequence.
In the case of alignment-ambiguous data, the effects of different underlying alignment algorithms on phylogenetic reconstruction are usually greater than the effect of the different inference methods.
As a consequence, the accuracy is usually even increased by limiting the size of base pairs (cf. [ 48].) Both, target T and query Q are sequences of nucleotides or, in the case of multiple alignment, alignment columns with lengths n and m, respectively.
Open image in new window Fig. 4 Schematic showing three possible cases of alignment of CAA with respect to MA Case 1 and 2 : β = γ + sin - 1 x / b ∗ sin α - γ / cos α Open image in new window (1) Case 3 : β = - γ + sin - 1 x / b ∗ sin α + γ / cos α Open image in new window (2 where.
