A major use of interspecies alignments is to transfer functional data from one species to another, making an alignment most useful if aligned functional regions have the same or analogous function in the two species.
However, other technical considerations are likely to be at least as important, such as the ease of sequence recovery, the frequency of DNA sequencing artifacts, and the question of whether DNA sequence alignment is useful for identifying species using barcodes.
The magnetic control of Schwann cell alignment is useful in medical engineering applications such as nerve regeneration.
This alignment proved useful for assigning specific amino acid variants within and/ or between species and to specific geographic locations of varying environmental conditions.
In this study, in silico PCR and BLAST sequence alignment proved useful for inferring the cucumber scaffold location of markers on the melon consensus map.
Intraoperative assessment of passive range of motion and CT imaging of the components' alignment proved useful for measuring in vivo tibial-femoral kinematics and objectively categorizing the nominal and outlier alignment groups after mobile-bearing TKR.
Measurement of knee alignment is useful in planning of operative intervention including high tibial osteotomy (HTO), uncompartmental knee replacement (UKR), and total knee replacement (TKR), and in the assessment of postoperative outcomes (Hernigou and Deschamps 2004, Hardeman et al. 2012, Kyung et al. 2013, Pietsch et al. 2013, Chen et al. 2014).
The number of species included in publicly available pre-computed multiple alignments continues to increase, which makes these alignments more useful, but also more difficult to analyze, as more species results in more fragmented alignments.
Many features of individual alignments are useful for sampling homologous sequences (e.g., alignment coverage, level of similarity, etc) but their organization and accessibility across the BLAST result page do not facilitate their interpretation.
For such twilight zone of alignments, various useful strategies have been developed to get reliable alignments.
