The phrase "alignment loci" is correct and usable in written English.
It can be used in contexts related to genetics, biology, or any field discussing the positioning of specific genes or markers within a genome.
Example: "Researchers identified several alignment loci that are crucial for understanding genetic variation in the population."
Alternatives: "alignment points" or "genetic markers".
We considered both alignment locus and read length in our definition of read duplication, allowing one read at each locus with a unique read length.
First, using a subset of terms from the Gene Ontology (GO Slim) [ 48] we grouped 2,158 alignments (loci) containing GO annotation into 27 broad classes as defined by their parent GO terms from the Molecular Function ontology.
After manual inspection of alignments containing nonsense SNPs, to filter out cases that could be explained by genome assembly problems, we ended up with 113 alignments (loci) with clear nonsense polymorphisms, many of which correspond to hypothetical proteins (80%, see Additional file 3: Table S3).
Based on the generated alignments, locus-specific primers were constructed, with the forward primer occupying a region 5'-end upstream of the insertion site, which is conserved among the colobine and human or chimp sequences.
To obtain the site rate distributions for each locus, two data entries are needed: (1) an alignment of loci of interest, pruned to contain a set of taxa for which the tree topology is fairly well known, and (2) an ultrametric tree for those taxa.
From the alignment, 90 loci distributed on 20 linkage groups of the newly developed linkage map were identified as having corresponding loci in the integrated consensus map (Additional file 3).
Alignment of loci within outlier regions to the rainbow trout genome and classification of gene functions identified possible targets of domestication selection.
On the basis of alignment, polymorphic loci against the reference sequence were identified according to the following criteria: Q ≥ 20, 3 ≤ Depth ≤ 100 and at least 5 bp away from each other.
One of the hallmarks of typical phylogenomic data sets is partial taxon coverage among loci by which we mean not merely missing nucleotides within an alignment but loci for which an entire sequence is missing for some taxa (Sanderson et al. [ 31]; also referred to as "taxon occupancy" by Hejnol et al. [ 10]).
