However, the correctness of the alignments generated by these methods is difficult to assess objectively since little is known about the exact evolutionary history of most proteins.
The knowledge of even one 3D protein structure in a given sequence alignment provides a powerful means to test the correctness of the whole alignment.
The structural conservation between the target and template, as well as the correctness of the template alignment, are among the most important factors in generating homology models.
To reduce the possible effects of LBA and correctness of the sequence alignment, we used the following approaches: (1) three taxa the most evolutionarily distant from M. leuckarti (M.
Since the introduction of mapping quality scores in MAQ (Li et al., 2008) to indicate the probability of the correctness of alignments, the concept of mapping quality scores has been frequently used in many NGS read aligners.
At the same time, the correctness of the model's alignment, again, highly depends on the footprint structure, so that, in some cases, even an additional small wall can resolve ambiguity of scaling parameters and thus the right model placement.
Our analysis relies furthermore upon the correctness of the pairwise protein alignments that serve as our data basis.
Generally, a higher mapping quality score indicates a higher confidence in the correctness of an alignment.
The biological issue surrounding MSAs is even more complex: given a set of sequences, we do not know how to estimate similarity in a way that will guaranty the biological correctness of an alignment, whether this correctness is defined in evolutionary, structural or functional terms.
To decide the correctness of reported alignments, we use the human rhesus pairwise alignments (rheMac2.hg19.all.chain) provided by UCSC.
