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Within each genotype, this region could be aligned unambiguously with a high degree of specificity, but alignment between genotypes was problematic.
OK, but "alignment" is a slippery concept.
Hinged external elbow fixation enables early mobilization after complex elbow dislocation and residual instability, but alignment of the fixator may cause complications and require revision procedures [6].
But alignment in what you believe and what you care about matters more.
Allow for extension through repetitive regions, but alignment isn't seeded in repetitive region (soft masking).
Alignment of the rht1 data set was unproblematic, but alignment of the sd1 data set showed that the three tef haplotypes contained short regions of sequence that were markedly divergent from the conserved positions in the other sequences.
Similar(50)
The genera of Microbotryaceae were not clearly resolved, but alignment-independent moderate bootstrap support was achieved for a clade containing the majority of the Microbotryum species.
It is usually labeled as 'pseudo-tRNA' by automated annotation pipelines, but alignment-based RNA folding analysis predicts a complete tRNA-Gly-like structure (Additional file 1 Figure S1).
In this way alignments spanning short repeats were not penalized, but alignments largely composed of likely repeats were removed.
Our initial intention was to estimate dN/dS ratios, but alignments were largely oversaturated with synonymous substitution rates (often inestimable).
Soft-masked means that seeds cannot intersect a masked interval, but alignments can be extended into and through masked intervals.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com