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The results show that the proposed algorithm is able to find a proper alignment despite using simple criteria for selecting the points-of-interest.
They also noted that eight out of ten cases developed varus alignment despite satisfactory intraoperative alignment due to metaphyseal comminution, and this was associated with development of progressive radiolucent lines around the prostheses [4].
The guideline from Zambia (2007), achieved good alignment despite having been published prior to the current WHO recommendations.
The presence of a great number of phylogenetic diverse sequences resulted in a highly informative alignment, despite its short length of 32 amino acid positions.
Moreover, as the algorithms are not amenable to massive parallelization, this makes the pair-HMMs not suitable for large-scale sequence analysis tasks, such as the whole genome alignment, despite their superior performance compared to other heuristic methods.
However, as RNA-Seq data sets come from fragment libraries of 50 bp reads, and given the heuristic nature of algorithms for reads' alignment, despite our checks, false-positive alignments may have occurred.
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Reducing the protein to a coarse metric such as secondary structure elements (SSEs) or structural fragments can also produce sensible alignments, despite the loss of information from discarding distances, as noise is also discarded.
A consensus of highly weighted suboptimal alignments was shown to contain pairs with significant probabilities that agree with structural alignments despite the optimal alignment deviating significantly.
An average of 28.3% SNPs failed to be detected from BWA alignments despite a higher accuracy in SNPs detected from both BWA and Bowtie alignments.
Furthermore, the fact that we can still see the phase 1 signal peptide peak in our start codon alignments despite the length variation of signal peptides suggests that the "dilution effect" does not completely wipe out peaks relatively close to the N-terminus, but only makes them broader.
Our phylogenetic assessment of orthology in these OBPs is robust across all alignment methods (despite moderate branch support in some cases), suggesting that the assignment is accurate.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com