The phrase "alignment coordinates of" is correct and usable in written English.
It can be used in contexts related to mathematics, computer science, or any field that involves spatial relationships or data organization.
Example: "The alignment coordinates of the two datasets must be adjusted to ensure accurate comparison."
Alternatives: "position coordinates of" or "alignment points of".
The alignment coordinates of uniquely aligned reads for each sample were used to independently calculate the read depth of each annotated gene.
This alignment looks for inversions by attempting to align the query gap sequence to the genomic region bounded by the genomic alignment coordinates of the bases flanking the gap in the original contig-to-genome alignment.
The program extracts the alignment coordinates of matching regions between the query and the corresponding database hit sequence.
The SuperGenome coordinate system is based on the alignment coordinates of all concatenated blocks, whose ordering is derived from the reference genome of the alignment.
The standard output by the web version of Panseq provides the alignment coordinates of each of the reference genomes against the pangenome sequence rather than against the input sequences.
On top, alignment coordinates and genome coordinates of the reference genome (mm9 in this case) are shown.
If the sequence length (not counting gaps) of the prediction in base pairs is called l, its start position in the alignment in alignment coordinates (i.e. including gaps) is called s and its end position in the alignment (in alignment coordinates) is called e, then the beginning is the region in the alignment from s to s + l (in alignment coordinates), and the ending is the region from e - l to e.
Exon templates were then inferred from EST alignment coordinates.
Finally, based on the alignment, the coordinates of the model were constructed for the structurally conserved regions of the model.
For each comparison, a report containing sequence identifiers, alignment length, coordinates of the most similar regions, percentage of identity, number of gaps, raw and bit scores and E-value was returned.
Spine then outputs DNA sequence and genomic coordinates of regions present in a user-defined subset of the reference genomes using the NUCmer alignment coordinate file and the sequences of the reference genomes.
