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Annotators are a lot like functions, except that they operate over Annotations instead of Objects.
Note that we might wish to completely marginalize over annotations and award gain only based on alignment.
The script used to perform this simulation and lift over annotations to the modified sequence is available at https://sourceforge.net/projects/kitchen-drawer/files/sim_SV.py/download.
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Kraken first identifies candidate regions for projection from the synteny graph and then performs an exhaustive alignment to return base-accurate lift-over annotations.
Over-annotation of genomes, resulting in an excess of small predicted proteins is clearly evident in certain genomes (e.g the initial annotation of Aeropyrum pernix [7]) and is proposed to be an unfortunate feature of many genomic annotations [6], [8], [9].
Since only a minority of genes (2.7%) were not active under any condition tested (null reads), we suggest that the assumption of significant genome over-annotations is wrong.
Over-annotation using KEGG suggests that this annotation type is especially sensitive.
Furthermore, there is no webserver or software specifically devised for the problem of over-annotation.
69.4% of the silent genes are hypothetical genes, indicating a potential over-annotation.
Such excesses of over-annotation equally affect the presumed non-catalytically active proteins and subfamilies.
Therefore, the risk of over-annotation is especially high for this genome.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com