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Both HMMER3 and PSI-BLAST [34] overcome this weakness by weighting mismatch penalties on the likelihood of a match for a given region (i.e. how conserved a particular region of the gene is).
The difference between orphan and non-orphan QIPP scores suggests that it might be possible to predict a priori how conserved a particular CDS might be using QIPP scores in the absence of homology.
Therefore, it is plausible that, as long as the recognition sequences are conserved, a particular site will not lose the ability to be edited, even though the C has been substituted by another base.
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For an enterprise it is perhaps not attractive to conserve a particular type of material through product multiple lifecycles approach which is naturally abundant but extremely important if the material becomes critical.
We also chose to examine the effect of position 86 as an example in which enzyme sequence is not conserved, but a particular property difference (in this case charged versus neutral) is conserved.
Thus, to expand our understanding of lineage-specific evolution, we identified HCNSs that were conserved in a particular lineage (either in primates or in rodents) and compared characteristics of the lineage-specific HCNSs with those conserved among mammals and vertebrates.
The repeat sequence is highly conserved within a particular CRISPR locus.
For instance, a residue that is conserved in a particular subgroup and is important for interaction with a specific partner, will have a high score in GROUPSIM, and mutation will probably result in lack of function.
The signatures were found to 98-100% identical and conserved in a particular species.
Hence, a site with a low functional entropy but high AA entropy suggests that it is conserved for a particular physicochemical property but not a particular residue.
Such comparisons are valuable in order to find genes for which the function is conserved for a particular process that may not be identified by other methods.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com