The phrase "alignment assembly" is correct and usable in written English.
It can be used in contexts related to engineering, manufacturing, or any field where components need to be aligned and assembled together.
Example: "The technician carefully adjusted the alignment assembly to ensure that all parts fit together perfectly."
Alternatives: "alignment mechanism" or "alignment setup".
If all overlapping transcripts yield consistent gene structures, they are assembled into a single alignment assembly, and by doing so, PASA acts to simply consolidate the transcript alignments into a single gene structure.
Wheat gene structures (exon-intron junction sites) were predicted by alignment assembly between 12 rice contig sequences (Pseudomolecules) assembled with a minimum tiling path of 3,408 BAC/PAC clones and rice cDNA models containing the untranslated region but no intron sequences.
All transcripts, including ESTs and FL-cDNAs were aligned to the genome, followed by our transcript alignment validation procedure and subsequent alignment assembly.
Such nanopatterns serve as model templates for the study of site-specific adsorption, alignment, assembly, and reaction of small molecules [8, 9, 11, 12] as well as macromolecules [13 16].
For these reasons, there is a need to integrate better models of sequencing error into a wide variety of sequence analysis methods, including alignment, assembly, gene finding, and phylogenetic modeling.
An individual alignment assembly was labeled as having a specific splicing variation as evident when compared to another alignment assembly supporting the variation.
The PASA-filtered transcripts were then anchored to the genome scaffolds by assembling overlapped transcript alignments into maximal alignment assemblies in order to remove multiple spliced isoforms.
PASA assembles overlapping and compatible alignments into maximal alignment assemblies; compatible alignments are defined as overlapping alignments that are transcribed on the same strand and have identical introns in their regions of overlap.
However, overlapping transcript alignments that have different introns in their region of overlap, due to a splicing variation, are found incompatible and cannot be assembled together, and hence occupy distinct maximal alignment assemblies.
We also assembled 369,092 spliced Arabidopsis transcript alignments into 29,183 alignment assemblies, of which 22,951 include FL-cDNAs (Table 1).
Using PASA, we assembled the 501,379 spliced rice transcript alignments into 43,869 alignment assemblies, 23,308 of which contain FL-cDNAs (Table 1).
