However, this accumulation of transformation may also result in the accumulation of small registration errors, and may, therefore, result in considerable large errors in the overall alignment for time steps that are "far away" from the common reference in the temporal succession.
When performing assembly for a group of reads in a given cluster, reads that do not fit well in the overall alignment are dropped out and not included in the final formation of the "contigs", the consensus sequence representing a cluster.
The change in the total score reflects the success of the treatment in achieving overall alignment and occlusion [ 14].
Hence we did not remove areas of uncertain alignment, especially since the AU plots of both the Solenopsis and Apis BAli-Phy alignments suggest that there are still high quality alignment blocks within these "problematic" areas to warrant their inclusion in the overall alignment procedure (Figure 1b).
Removal of length polymorphism at three mononucleotide repeat regions from the chloroplast trnS- trnG alignment resulted in an overall alignment length of 495 bp and seven distinct haplotypes (Table 3; Figure 2; GenBank sequence accession numbers HQ864688- HQ864694).
The authors demonstrated in this study that TKR performed with computer navigation yielded similar postoperative results in terms of overall alignment, even when there were variations in surgical experience.
There are three causes of failure of HTO in a varus knee: inability to correct the deformity during surgery, a "tibial teeter-totter effect" (advanced medial tibiofemoral OA and obliquity), and gradual collapse of the medial compartment over years, in which the overall alignment drifts back to varus because of continued medial tibiofemoral OA [28].
Even when only a small fragment of the adapter is overlapping, as shown in (C), the overall alignment is easily sufficient to ensure reliable detection.
An alternative approach for treating correlations between conformations and overall alignment in systems dissolved in ordering media involves using programs such as PALES or PATI that compute the alignment based on molecular shape (and electrostatic properties).
There are five molecules in each asymmetric unit; overall alignment of the backbones of the five molecules is shown in Supplementary Figure S1(A) at http://www.biochemj.org/bj/450/bj4500085add.htm.htm
