The phrase "alignment list" is correct and usable in written English.
It can be used in contexts where you are referring to a list that outlines alignments, such as in project management, data analysis, or software development.
Example: "Before we proceed, please review the alignment list to ensure all team members are on the same page regarding project goals."
Alternatives: "alignment chart" or "alignment overview".
The following steps are done until the convergence of the alignment is fulfilled: 1) For each pair of the matched SSEs, put the start and end residues as temporarily aligned pairs in the alignment list.
4) Make and apply the rotation matrix based on the aligned pairs of residues in the alignment list.
Moreover, the algorithm clears the alignment list for each repetition, and looks again for the alignment.
2) For each pair of the matched SSEs, find n neighboring residues (n is chosen 3 for strands and 4 for helices [ 6]) having minimum distance, put them in the alignment list, and then, extend the alignment to the ends of the elements.
The accession numbers of all the TGA proteins used for sequence alignment are listed in Additional file 2: Table S1 Fig. 2 Phylogenetic relationship of LhSorTGA2 with TGA family proteins from other plants.
The reference sequences that were used for the alignment are listed in Table 2.
The GenBank accession numbers of the sequences chosen for alignment were listed in Table 2.
The sequences taken from each alignment are listed in the second column.
Here the approach suffers from the same problem as DIALIGN, which is, however, resolved in a different way: instead of producing a single locally optimal alignment, TRACKER lists all maximal compatible sets of pairwise alignments.
The mitochondrial and nuclear regions used in the bird alignment are listed in Table S4, which also gives the GenBank accession numbers of the downloaded sequences added to the alignment using the Mesquite software [ 35].
Again, most of final models had a higher TM-score than that of the best threading alignments (a list of the best templates with the highest TM-score for each target protein in this study is available online at ).
