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Distributions were directly represented on the screen by scaling the color axis by screen position between blue and green according to the probability that a star would be generated in the given position.
In the same gene family, old introns were embedded within strong protosplice motifs which were found to be much weaker in homologous genes lacking the intron in the given position [ 123].
Protein sequence motifs were represented using sequence LOGOs where the height of the amino acid symbols is a function of the frequency of the given amino acid in the given position [ 54, 55].
To quantify ectopic expression, we ranked for each OR gene the ectopic tissues according to their expression level, then for each ranked position we calculated the mean expression intensity and the entropy, which reflects the diversity of tissues in the given position.
The assumption is that any character shared by the majority of eukaryotes and the 10 diverse prokaryotes (the outgroup) is the ancestral state, and accordingly, the species with a substitution in the given position possess a derived state (one, two or three nucleotide substitutions are allowed, Figure 1).
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I needed to give, but the biggest gift I could offer seemed to be allowing others to be in the giving position, too.
Proteins are chains of amino acids, and if all the parent genes code for the same amino acid in a given position in the chain, then all the offspring will as well.
Rows 2 5 show the profile (the frequency of observing a DNA base in a given position), and the last row shows the corresponding pattern over the IUPAC alphabet.
Figure 7 Mutual information between the next move in a given position and the position itself.
A motif is reported for a stretch of three or more consecutive positions with complete conservation or favorable substitution (based on an identical or similar residue in a given position in the MSA and the average score).
In addition, we studied the modification level distribution (the fraction of cDNA reads exhibiting the modification in a given position) for both types of modifications.
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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