The phrase "alignment threshold" is correct and usable in written English.
It can be used in contexts related to measurement, standards, or criteria for determining alignment in various fields such as engineering, data analysis, or project management.
Example: "We need to establish an alignment threshold to ensure that all components fit together properly in the final assembly."
Alternatives: "alignment criteria" or "alignment standard".
Mismatch and gap parameters were set to 0.3 and the local alignment threshold was set to 2.0 [2.0.
Putative orthology relationships between the two genomes were defined by gene pairs satisfying either the Bidirectional Best Hit criterion [90] or an alignment threshold (at least 40% sequence identity over at least 80% of the length of the smallest protein).
Putative orthologous relations between two genomes are defined as gene pairs that satisfy either the Bidirectional Best Hit criterion [69] or an alignment threshold (at least 40% sequence identity on at least 80% of the length of the smallest protein).
Overlapping alignment threshold was arbitrary set at 7 nt.
The column between the dendrogram and the heatmap represents the probesets either differentially expressed and selected with the 70% perfect alignment threshold (yellow), or the probesets differentially expressed but not selected by the Perfect Alignment threshold (black).
The alignment threshold was set to a maximum of three nucleotides mismatch between Illumina reads and the reference.
Without using alignment thresholds, more than 99.9% of all sequences could be aligned back to the reference.
The size of this fraction may be exacerbated by the relatively conservative alignment thresholds applied during our analysis.
Alignment thresholds were specified which allowed up to three base pair mismatches between the 80 bp Illumina read and the reference (>95% identity).
Due to the interaction between the circular nature of many genomes and chosen alignment thresholds genomes shorter than 1700 nt were removed from further analysis as there is the possibility that their maximum contig coverage may have been slightly underestimated.
It is fundamentally different from other methods because it is free of the parameters which govern local alignment, thresholding between targets and non-targets, and any distinction between conserved and non-conserved instances of individual binding sites.
