In 3D model retrieval, preprocessing of 3D models is needed, in which alignment is a key factor that significantly affects retrieval performance.
Second, in the context of a resequencing project, variant detection is ultimately a process in which alignment is only the first phase, and which could employ diverse analytical methodologies, such as local reassembly, to return final variant calls.
Automated alignment for each protein was performed using ClustalX [ 58], after which, alignment was manually adjusted with MacClade 4.06 [ 59].
Lowering the identity threshold below which alignment is refused by PyNAST to 0.0001 reduced the number of failed alignments.
The first approach, economic integration, is rooted in the economic literature, in which alignment is realized by financial means.
For read pairs in which alignment was still not found for both reads, the reads were trimmed to 50 bp and aligned using '-n 0' again.
The first approach is rooted in the economic literature, building on the model of the homo economicus, in which alignment is realized by 'hard' financial means (economic integration).
This data implies the Archaeal ancestor of EF-2 had a 4 residue derived insertion regardless of which alignment is used.
In addition, by GUIDANCE filtering [ 81], the PRANK alignment has a higher average GUIDANCE score of 0.70, while the MAFFT, MUSCLE and CLUSTALW alignments is 0.65, 0.63 and 0.66 respectively, though the GUIDANCE cannot tell which alignment is better.
Nevertheless, even calculated structural alignments, if standard structure alignment procedures are applied, may be inaccurate: for some compared proteins, or regions therein, more than 1 possible superposition can reasonably be reported, and it may be difficult to decide which alignment is most satisfactory.
