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We also showed a very low/not significant correlation between the levels of MFE related signal conservation and corresponding sequence variability values, demonstrating that conserved selection for local folding strength across different genotypes cannot be trivially explained by lowly-variable patterns in the synonymous codons and/or nucleotides preferences.
If introns containing these signals are conserved, selection against their loss would result in the pattern that conserved introns have lower nucleotide substitution rates than lost introns.
Finally, we found no significant correlation between the levels of sequences variability and the levels of conservation of MFE signals, supporting the conjecture that positions with a conserved selection for strong/weak folding may be related directly to biophysical attributes of gene expression regulation and/or viral replication via folding.
Although the basal ganglia are thought to play a key role in action selection in mammals, it is unknown whether this mammalian circuitry is present in lower vertebrates as a conserved selection mechanism.
Conserved selection for strong / weak folding related signals cannot be explained basing only on dinucleotide composition.
These results support the conjecture that the conservation of MFE related signals is not necessarily and only due to a preference of specific synonymous codons or conserved nucleotide content, and cannot be solely explained by the low sequence variability, thus supporting the evidence for a direct, conserved selection on positions for strong / weak folding.
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Given this neutral background, we take two approaches to identifying sequences conserved by selection.
The sharing of MHC alleles among populations also indicates that MHC alleles may have been conserved by selection [ 19].
Based on primary and secondary structure comparisons, this helix in Vps1 is well conserved making selection of charge-switch mutations straightforward.
Microsatellites make up ∼3% of the human genome, and there is increasing evidence that some microsatellites can have important functions and can be conserved by selection.
DUX4 related sequences are found in primates and Afrotheria and we previously showed that they have been conserved by selection[ 1].
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