Overextension occurs more frequently in higher identity alignments because of target identity mismatch, but the majority of overextension we measured occurs by chance in low identity alignments, because most of our alignments are low identity.
If this is applied, the phylogenetic relationship between the new sequences and the sequences in the existing alignment cannot be considered, and thus, the alignment quality is low.
An inherent issue with alignment-based methods is low coverage due to emphasis on only conserved modules along with sensitivity to errors in network topologies.
Despite the sample obtained from DB110 strain grown at 0.1 MPa gave a high number of reads, the number of those having a single alignment is quite low; we hypothesize this could be due to a lower efficiency in rRNA depletion during the preparation of this sample.
Finally, in the bottom right quadrant, in countries as Slovakia, Hungary, Greece and others, the majority of south-eastern Europe, there is low alignment between old age related expenditure and elderly needs, though formal care is slightly above the mean.
One major conclusion is that iterative alignment programs clearly outperform progressive alignment programs, particularly when sequence identity is low and more than five sequences are aligned.
Approaching sequence analysis by analyzing the distribution of succession patterns, which is to say, of L-tuple (oligomer) frequencies [ 9], is advantageous when the sequence similarity is low because alignment algorithms cease to recognize common motifs that are inexactly conserved, as recently illustrated for the SCOP protein database [ 10].
The precise reason for this effect requires further investigation but it is possible that when the level of antibody attachment is low the alignment of the antibodies are less ordered so that they provide a less favorable orientation to the binding proteins.
