The phrase "alignments for the same" is not standard and may be unclear in written English.
It could be used in contexts where you are discussing alignments related to a specific subject or item, but it lacks clarity.
Example: "We need to establish the necessary alignments for the same to ensure consistency across the project."
Alternatives: "alignments for this" or "alignments regarding it".
Results from multiple structure alignments for the same domain pair are averaged over the domain pair.
To emphasize, overlapping denotes some coverage of common sequence ranges between the two alignments for the same domain model.
Instead, SAMBLASTER marks duplicates in a single pass over a SAM file in which all alignments for the same read-id are grouped together.
Multiple alignments for the same sample were combined by the use of BamTools (Barnett et al. 2011) into a single alignment.
In this instance, NanoOK takes the highest scoring alignment and merges this with any alignments for the same reference that map close to the initial alignment.
Because breseq uses read mapping options that report all alignments to sequence repeats in the reference genome, pairs of alignments for the same read that match different reference locations may yield equivalent junction sequences but different junction descriptions.
To account for this, we filtered out alignments that are overlapping on the reference with another alignment for the same query.
Finally, the consistency score (S c ) can only be computed when more than one alignment for the same set of sequences is provided.
Detailed table list with the best inferred substitution models using JModelTest software for the alignments of the sequence data generated in this study for UL18, UL22, UL27 markers and for the alignment of the same dataset for UL27 plus all the available sequences at GenBank database.
The reasons for choosing a limited set of control genes were two-fold: first, this allowed us to generate manually curated alignments of the same quality as for the CT genes, and second, it provided test and control groups of similar sizes for statistical analysis.
Re-computation of alignments for largely the same sets of sequences is wasteful and may occasionally introduce errors that require manual verification and corrections.
