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The explosion of protein sequences deduced from genetic code has led to both a problem and a potential resource: Efficient data use requires interpreting the functional impact of sequence change without experimentally characterizing each protein variant.
These results underscore the importance of evaluating the impact of sequence context on the activity of therapeutic group I ribozymes.
We investigated the impact of sequence sample size on entropy calculations by random subsampling from a set of 499 sequences.
To assess the impact of sequence divergence on multiple alignment accuracy we first compared the alignments from Muscle with the true INDELible alignments.
This procedure was adopted to avoid the overestimation of prediction accuracy and reduce the impact of sequence or domain homology on the prediction performance [58].
To assess the impact of sequence alignment, RAxML trees were also inferred under the same settings from the other alignments, an approach known as multiple analysis [64], [65]; for details, see supporting file S3.
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To eliminate the impact of sequencing depth and sequencer bias on the WGA comparison, we randomly extracted 0.1X data from the raw LWGS data (Additional file 4: Table S4).
Anvi'o relies on a heuristic to identify SNVs that sets a minimum baseline that varies as a function of coverage depth in order to minimize the impact of sequencing or mapping error55 (the URL http://merenlab.org/2015/07/20/analyzing-variability/ gives access to a tutorial).
The explanation may be related to the lower temporal resolution of 3D-cine, which reduces the accuracy in the selection of the proper end-systolic phase compared with the 2D-cine sequence; this is in agreement with previous studies exploring the impact of sequences with low temporal resolution [22].
It is interesting to imagine the impact of sequencing additional cells.
Finally, we examined the impact of sequencing error on inferred rates and patterns of insertion/deletion and substitution on the mammalian phylogeny.
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