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They also introduced some scoring rules of alignment to separate the seed region from rest of the regions as well as relaxed values for mismatches and wobbles.
For example, for non-coding sequences of plastid genomes special rules of alignment were developed and this increased resolution and reliability of phylogenetic trees inferred from these sequences [ 47, 48].
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To further disclose the underlying mechanisms of protein β-sheet formation, studies were made on the rules of β-strands alignment forming β-sheet structure using statistical and machine learning approaches.
miRanda [20], [29] is the first microRNA alignment algorithm, is similar to the Smith-Waterman algorithm for sequence alignment and uses rules of thumb previously established in sequence alignment [50], [51], [52].
The correlation of allele frequency scores between BWA and Bowtie were very high, indicating that strand bias is not likely due (although not completely ruled out) to the artifacts of alignment, but is more likely an artifact or due to errors from the library preparation or sequencing.
The average bootstrap value on the majority rule consensus tree was plotted as a function of alignment length to evaluate how data availability affects tree resolution.
Currently, that type of alignment is the exception rather than the rule.
To derive pronunciation variants, we extracted context-dependent rewrite rules from an alignment of canonical and realized phonemic representations of non-native speech from the JASMIN corpus (the test material was excluded).
The monitoring model of alignment between MPU and propulsion shafting is established, followed by the alignment control algorithm and converge rule which assures the fast and uniform convergence of both air springs׳ load distribution and alignment control process.
Or out of alignment".
"I'm all out of alignment".
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com