The phrase "alignment is denoted" is correct and usable in written English.
You can use it when explaining how alignment is represented or indicated in a specific context, such as mathematics or design.
Example: "In this diagram, the alignment is denoted by dashed lines connecting the elements."
Alternatives: "alignment is represented" or "alignment is indicated".
Conserved amino-acid positions in the protein alignment are denoted with '*' (b) Representative 3D-structural model, using I-TASSER prediction server, of the 37-F6 caproteinotein compared with the nearest viral capsid proteins: the Tara Contig 67SUR_4106 and viruses from SAGs AAA160-P02 (Flandbacteria) and AAA164-I21 (Verrucomicrobia).
Let the set of nucleotides at position i in the alignment be denoted q i and the nucleotide in the ancestor at position i be denoted α i.
Then, the alignment can be partitioned into two separate parts as follows: Let these partial alignments be denoted as A (T 1, …, T 10 ) and A (T 10, …, T 15 ), identifying the start and end residue indexes in T about which the partition is defined.
④ All alignments of Exon i is denoted as stage A i. The alignment being studied is called " state" (denoted as s i ), and s i = j means the j th alignment.
In this article, the space of all pairwise alignments of x and x′ is denoted by 𝒜 x, x′).
In addition the set of breakpoint intervals for the paired-end read alignments in set ape i is denoted as Br i ={(Br i 1 L, Br i 1 R ), (Br i 2 L, Br i 2 R ),…, (Br i m i L, Br i m i R )}.
A read spanning multiple regions, e.g. multiple exons, is denoted by multiple alignment blocks that are separated by a comma.
Moreover, a space of structural alignments of two RNA sequences x and x′ is denoted as 𝒮𝒜(x, x′).
An alignment of a read pair to the reference genome is denoted as concordant (Tuzun et al., 2005) if the distance between the aligned end reads is in the range [Δmin, Δmax] and the alignment orientation is +−.
Consequently, every site in the alignments, called pattern, is a vector of length S over the alphabet (0,1,*) and is denoted by ω.
