In cases where we encountered multiple high scoring transcript hits against the genome, we manually looked into the alignments to rule out the occurrence of pseudogenes that frequently lacked introns when compared to the "true" genes.
C. Misale et al. in their paper entitled " Sequence alignment tools: one parallel pattern to rule them all?" are engaged in NGS and investigated the performance of the widely used alignment tools Bowtie2, BWA, and BLASR.
Nevertheless, in the absence of in silico results, or if pathogenicity is indicated by only one alignment analysis, the MMR proficiency is not sufficient to rule out pathogenicity.
To allow for smooth alignment, all co-builders work together in the planning phase to rule out unwanted conflicts between work activities.
To rule out HGT in well-supported conflicts, we scrutinized the alignment in more detail, increased taxon sampling, and tried other models and phylogenetic methods.
To rule out the effects of various protein sizes, in implementation the alignment size was normalized by the protein size with Formula 3 and was thus called the alignment ratio (unit: percentage).
Expect pragmatism to rule.
They also introduced some scoring rules of alignment to separate the seed region from rest of the regions as well as relaxed values for mismatches and wobbles.
Something is out of alignment, to be sure.
