The phrase "alignment return" is correct and usable in written English.
It can be used in contexts related to data analysis, programming, or any field where alignment and return values are relevant.
Example: "The algorithm's alignment return indicates how closely the data matches the expected format."
Alternatives: "alignment output" or "alignment result".
BLAST performs local alignment, returning the start and end of the alignment (the hit) for the query sequence and the target sequence, as well as the E-value.
In the read 1 example, the expected alignment starts in 4031012 and ends in 4031103, with two deletions, no insertions; and one substitution; however, the alignment returned by the mapper starts in 4031014, ends in 4031103, and showed only one substitution.
The alignment returned by LOCK2 is a sequence of pairs of points (6) (a i 1, b i 1 ), …, (a i k, b i k ), i 1 < ⋯ < i k, where a i r are b i r each other's nearest neighbors.
In contrast, the overlapping alignments returned by Adaptive GDDA-BLAST depict the domain architecture of 1N11 with all 12 Ankyrin-repeat domains predicted (pink line in Figure 4-b).
The four cytochrome b alignments returned very similar results.
The alignments returned by RINQ are statistically significant and biologically relevant.
This utility performed a pair-wise Smith Waterman overlapped alignment (Smith and Waterman, 1981) between reads pairs, and selected the best quality base where alignments returned mismatching bases.
Note that GO terms are not used for computing the alignments and can only facilitate the understanding of the alignments returned by GASOLINE.
They only give, when provided by the user, useful information to better understand the final set of local alignments returned by GASOLINE.
In other situations, the numerical scores of biologically correct alignments turned out to be below the scores of biololgically wrong alignments returned by the non-anchored version of our program.
