The phrase "alignment chain" is correct and usable in written English.
It can be used in contexts related to organization, processes, or systems where elements are aligned in a sequence or hierarchy.
Example: "The alignment chain in our project ensures that all team members are working towards the same goals and objectives."
Alternatives: "alignment sequence" or "alignment network".
Comparisons of computational speed with respect to the literature is somehow difficult to infer since (1) not every work declare computational speed, (2) only isolated blocks of the alignment chain are usually considered (e.g. feature extraction) instead of the entire pipeline, (3) hardware obsolescence.
We annotated noncoding blocks based on the alignment chain they reside on compared with the exons of duplication peptides within 5 kb.
Using human macaque alignments, we annotated each DA block as either chained (same alignment chain as the gene's exons) or nonchained (all other DA blocks; see Materials and Methods and fig. 1).
When inspecting human chromosome 1 in the UCSC browser in the three selected regions, a similarity to sequence from the chicken E26C13 linkage group was found in the chicken alignment chain and alignment net tracks around position 147.5 Mb of HSA1.
Conservation of tandem sites was detected by analyzing the genome-wide pairwise alignments downloaded from the UCSC genome browser (assemblies: human hg17, chimpanzee panTro2, rhesus rheMac2, mouse mm7, dog canFam2, chicken galGal2) using the genomic locus of the human tandem sites to select the respective alignment chain.
Assuming co-occurrence on an alignment chain indicates duplication of the noncoding sequence with the gene, this finding suggests that the derived (i.e., daughter) noncoding sequence is more likely to diverge from the ancestral version than the copy that remains at the parent locus.
For closer evolutionary distances, the alignments are created using syntenically filtered BLASTZ alignment chains, resulting in a prediction of the orthologous genes in cow.
These alignments were then processed using the UCSC alignment "chains and nets" pipeline (Kent et al. 2002) to eliminate paralogous alignments and identify regions of conserved synteny.
The pairwise alignments are cleaned either by synteny (small alignment chains are deleted when they would otherwise break synteny) or by deleting all but the best alignments where the target genome is multiply-covered.
At UCSC, the Nanog upstream region does not feature a high-coverage 30-way Multiz alignment (see Figure 6); in case of human, chimp, orangutan, rhesus and cow, individual alignment chains compensate.
We observe that crystal nucleation is initiated by the alignment of chain segments, which is followed by straightening of the chains and densification.
