The phrase "alignment defined as" is correct and usable in written English.
It can be used when explaining or clarifying the meaning of "alignment" in a specific context or framework.
Example: "In our study, alignment defined as the degree to which team members share common goals is crucial for success."
Alternatives: "alignment described as" or "alignment characterized as".
Cell alignment, defined as the angle between the long axis of a cell and the long axis of its nearest neighbor, and projected cell area were independent of the distance between cells and the fibrinogen concentration (Fig. 7A and 7B).
As a result we argue that clinical integration is an outcome of alignment, defined as the degree to which physicians and hospitals share the same mission and vision, goals and objectives, and strategies, and work toward their accomplishment [ 9].
For each LOMETS program, a Z-score cut-off (Z0) is assigned, based on the threading results data of 1190 independent training proteins, so that the well-defined alignments with an average TM-score >0.6 can be achieved when Z-score > Z 0. Here, Z-score is a measure of the significance of the target-template alignment, defined as the score difference to the mean in the unit of standard deviation.
The distance between the modes of the forward and reverse peaks in the alignments, defined as ' d', was 152 bp for the LRH-1 ChIP-seq data.
To study the peptide evolution in X. laevis paralogs further, we identified 148401 highly-constrained positions in the six-way LLTHMR multiple alignments, defined as positions with an identical amino acid in human, mouse, rat and at least two of the three frog orthologs.
More formally, the coverage of an alignment of length N mat is defined as, where | A| is the length of protein A, similarly for | B|.
PASA assembles overlapping and compatible alignments into maximal alignment assemblies; compatible alignments are defined as overlapping alignments that are transcribed on the same strand and have identical introns in their regions of overlap.
A suboptimal alignment was defined as any alignment which exceeded 3 standard deviations of the mean pairwise genomic divergence (window size 2 kb, slide 100 bp).
A suboptimal alignment was defined as any alignment which exceeded 3 standard deviations of the mean K2 divergence (window size 2 kb, slide 100 bp).
In Prefab, the reference alignment is defined as the portions of alignments consistently aligned by two structural aligners: CE (Shindyalov and Bourne, 1998) and DALI (Holm and Sander, 1995).
The quality of sequence alignments was measured by alignment sensitivity defined as | N ∩ S | / | S |, and precision defined as | N ∩ S | / | N |, where N is the set of residue pairs in the sequence alignment, and S is the set of residue pairs in the reference alignment.
