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And we all translated in chorus: "Be grateful for this never-to-be-repeated moment".
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We submitted all translated sequences (starting with a Met) to the Signal P server [ 97] to detect signal peptides indicative of secretion.
For each codon, we identify all translated regions in the genome where a particular codon (say CTC) occurs uniquely within a window of 10 codons upstream and 10 codons downstream that is, a window 19-codons wide, with the codon of interest occurring exactly once at position 10 of the 19-position window.
We have not checked explicitly if the proteins we used were all translated using the standard genetic code but a few exceptions would certainly not affect our results.
In order to analyze and compare the sequences we identified, we translated all of the cDNA sequences into protein sequences using the Translate Tool from the ExPaSy server [ 53].
To assign these spectra to peptide sequences, we created a database comprising all translated stop-to-stop amino acid sequences of more than forty residues, taking into account the six-frame translation of the genome of R. pomeroyi.
Therefore, we used all the translated amino acid sequences (the.faa files with NC_accession numbers) from NCBI.
To identify possible in frame translations of a given chimera, we translated all the chimera transcripts in six frames.
To do this, we translated all the P. yoelii genomic sequences downloaded from Genbank in all six frames and extracted all stop-to-stop open reading frames (ORFs).
Then, we translated all the sentences of Bosque using the prototype system and calculated the values of WER and BLEU based on the reference translation.
To combine the data from ChIP-seq with co-expression queries, we translated all the results into Ensembl gene identifiers using g Convert (Reimand et al., 2007).
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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