The phrase "alignment generated by" is correct and usable in written English.
It can be used when discussing the results or outcomes produced by a specific process or system, particularly in contexts like data analysis, machine learning, or organizational strategies.
Example: "The alignment generated by the new algorithm significantly improved the accuracy of our predictions."
Alternatives: "alignment produced by" or "alignment created by".
Then, the following conservative approach was taken to retain only unambiguously aligned sequences: Using the protein alignment generated by BLAST as a guide, a sequence pair was scanned to the right of each alignment gap.
The output BAM file, a standard format for sequence alignment, generated by a short read aligner may be created in different locations, or the output may not be stored in BAM at all.
The best-scored whole ITS alignment generated by SATé featured 300 taxa and 1,296 aligned positions, including 191 constant characters, 210 parsimony-uninformative changes, and 895 (69%) parsimony-informative positions.
First, a multiple sequence alignment generated by Buzko and Shokat [1] was adopted and binding site residues were identified.
The coevolved mutation analysis by PSICOV using multiple sequence alignment generated by PSI-BLAST and machine learning-based algorithm outputs are combined to generate the final predictions.
The target-template alignment generated by MODELLER agreed with the secondary structure alignment (Supplementary Fig. S1A).
We compared sequence alignments with the structural alignments generated by Fr-TM-align (Fig. 5A and B) and DaliLite (Fig. 5C and D).
In the Sisyphus benchmark, these superpositions increase the accuracy of alignments generated by STRUCTAL, TM-align, and LOCK2 by 11%, 7%, and 6%, respectively.
Although agreement was not exact, most Mulan aligned sequences coincided with the alignments generated by AVID and BlastZ (zPICTURE), and with MEME detected motifs.
To assess the alignment quality, we compared sequence alignments with the structural alignments generated by Fr-TM-align (Pandit and Skolnick, 2008), which allows flexible alignments, and DaliLite (ver. 3.3) (Holm et al., 2008) as reference alignments.
Similarity of the potential domains was assessed from structural alignments generated by DaliLite [28], wherein we considered the aligned residues to define conserved regions of a domain.
