The phrase "alignment category" is correct and usable in written English.
It can be used in contexts related to classification, organization, or categorization of items based on their alignment or compatibility.
Example: "In our analysis, we identified several alignment categories that help us understand the relationship between different variables."
Alternatives: "alignment classification" or "alignment group".
Using this approach we could determine that alignments where the Arabidopsis lyrata sequences lack a start codon and contain no indels or internal stop codons are the most frequent alignment category representing 53.66% of cases.
In contrast, the least frequent alignment category (i.e. evolutionary model) is where there are alignments with a start codon in the Arabidopsis lyrata sequences but containing either indels or internal stop codons, representing 12.06% of all cases.
MegaBLAST identified 435 FAexp Arabidopsis gene models (for which expression profiles were present in the Genevestigator® Meta-Analyzer) in the At_CD database with significant similarities to FAexpTRL and present in the top 10% (red zone) average monocot % alignment category.
In this analysis, there were 3057 FAexpTRL from Pm1, 2, 3, 4, 5, 7, 8, 9 and 10 which were in the top 10% (red zone) for the average monocot % alignment category and which also had significant alignments with all 4 monocot test databases (i.e. an average score of 1, see Materials and Methods).
In comparison, there were 508 different FAexpTRL from Pm1, 2, 4, 6, 7, 8, 9 11, 11 and 12 which were in the bottom 10% (dark blue zone) for the average monocot % alignment category and which also had no significant alignments with any of the 4 monocot test databases.
The other alignment categories indicate the number of probes that had a specific alignment.
Since knee alignment have great impact on biomechanical force transmission which may influence the degree of extrusion, a larger sample allowing enough numbers in different alignment categories would be valuable in future work [ 34].
However, when we performed RRT between non-rearranged (Hemisus, Limnonectes, Lithobates, and two Microhyla) and rearranged ranoids, significant substitution rate differences were not observed in any of the five alignment categories compared here [ P = 0.07 (all mt genes) to P = 0.8 (12S rrn)].
The final result was 299 orthologous protein alignments (categories 1 3 above), which were then re-aligned using MUSCLE before indel extraction.
The images were chosen such that the aligned category had the best possible coherent alignment, and the not-aligned category had a completely random distribution of nanowires, i.e. zero coherent alignment.
The scores for the aligned category by image classification are compared with a normalised value for alignment (coherency) using the OrientationJ plugin on ImageJ.
