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Initially, we wanted to test the value of this approach by focusing only on a limited section of sequence that should comprise a region of slow translation and whose usage frequency during heterologous expression would be strongly discordant.
Rather it is a continuous section of sequence located within the DBLα domain that is being maintained, which can be exchanged among paralogs as a unit by recombination.
Using the data from MRSfinder, MRS locations were plotted on a section of sequence extending 1000 bp upstream of the translation start site (ATG codon) through the first 400 bp of the coding sequence (CDS) from each C. elegans gene.
Sequencing of this region highlighted a synonymous single base change (T→C) within the coding sequence of exon 3 (see Figure 2), and a 160 bp section of sequence immediately upstream of exon 3 present in SHR but not WKY.
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This is found over a wide cross section of sequences, from e.g., the members of the globin family, the histones, tubulins and heat shock proteins.
In the final step individual domains of candidate agrin sequences were used as query to test whether in BLAST searches of vertebrate sections of sequence databases they give the lowest E-scores with agrins.
These points are just the important golden sections of sequence.
Gaps within the scaffolds, i.e. between sections of sequence, are represented by inserted N's, and the total length of elucidated sequence is ∼1.5 billion base pairs.
The folding 3′-end points of the sequence are almost close to 0.382 L, 0.5 L, 0.618 L, and L. These points are the important golden sections of sequence.
To identify the effects of local areas of extreme nucleotide composition, mononucleotide randomisation was applied to smaller sections of sequence (10 bp, 100 bp, 1 kb, 50 kb, 2 Mb and the whole chromosome length) to C. elegans chromosome I.
Interestingly, though, in most of these cases only a section of the sequence (not the full sequence) was present in the WGS suggesting this is an upper estimate of the number of false negatives.
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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