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The effect of increasing number of alignment sections is also analyzed.
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On the other hand, the MD method requires the inference of the missing state at each gapped site (or the summation of the likelihood for all four nucleotides at the gapped sites), a process that is bound to be strained with increasing number of gaps in the alignment.
The same is true for RNA alignments: with increasing number of sequences and decreasing sequence homology iterative programs perform relatively better compared to non-iterative approaches.
Taking advantage of the increasing number of sequenced mammalian genomes, we generated an alignment of repeat A sequences from 27 mammalian species (Additional file 2: Figure S2A).
First, taking the four methods together, there is a clear relationship between the proportion of indels and the estimated d N and d S values, which is consistent with previously reported alignment inaccuracies with increasing number of indels (see previous section).
In order to compare the increasing number of structures in the PDB, flexible geometrical alignments are needed, that are reliable and easy to use.
With increasing number of sequences and decreasing sequence identity the progressive alignment approach is more likely to introduce errors, which cannot be corrected at a later alignment stage ("once a gap, always a gap" [ 37]).
Recently, the rapidly increasing number of sequenced genomes enabled evolutionary studies relying on multiple-sequence alignments [ 19].
Additionally, the increasing number of sequences in the biological databases is perceived as one of the upcoming challenges for alignment methods in the nearest future.
So are an increasing number of foreigners.
"And an increasing number of traders.
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