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Inspection of the alignment and comparisons to similar alignments produced using CLUSTALW [ 16] showed that the MUSCLE alignment was better at correctly aligning the zinc coordinating amino acids and fewer manual adjustments were required than with CLUSTALW results (data not shown).
This is an interesting result that would require further research: at first sight it suggests that professors are correctly aligning their learning outcomes and assessment methods, and that the TALOE web tool identifies this alignment.
In transgenic embryos which were HS treated at 28 hpf, most if not all neuromuscular synapses were restored, with the majority of postsynaptic AChR clusters correctly aligning with the presynaptic nerve terminals (Figure 4B5 B6).
Paralagous genes in the poplar genome that arose from the salicoid whole-genome duplication event, as well as tandem gene duplication, may create problems both for the physical process of capturing fragments of genomic DNA, as well as correctly aligning the resulting sequence data.
Because of the high degree of paracentric inversions present in this species, the order of the genetic and physical markers already established in many cases differs from that occurring in the Gd-H4-1 lineage (Schaeffer et al. 2008), which emphasizes the importance of establishing physical markers in the sequenced lineage and correctly aligning their genomic and cytological maps.
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On average, in the 10 25% sequence identity range, alignments are improved by 28 correctly aligned residues compared with alignments made using FUGUE's default substitution tables.
Finally, pairwise LCBs in the predicted alignment lacking any correctly aligned nucleotide pairs are False Positive (FP).
In this example, 9 residues are correctly aligned over a total alignment length of 10 residues.
Table 6 gives the number of correctly aligned residues across all the alignments in each sequence identity bracket.
The best specificity was demonstrated by GMAP with almost 99.5% of introns matching those found in the mRNA alignments, followed by Splign that correctly aligned 98.9% of introns.
In terms of correctly aligned RI pairs, our multi-view alignment reaches a 99.7% performance.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com