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Interestingly, when we looked at SNVs, which had been already annotated in the dbSNP database (referred to as 'known SNVs'), the concordance rates are even higher reaching about 99% at 3× coverage.
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Of these, 20 sites were already annotated in CDD.
Out of these sites, 12 were already annotated in CDD.
PhosphOrtholog added 60%% of the common sites, and the remaining 40%% were already annotated in PhosphoSitePlus.
Authors' response: We acknowledge that these examples are already annotated in many genomes with the associated function.
For example, we looked if the predicted ends not annotated in the RefSeq database were already annotated in the Ensembl database and vice versa.
It would be interesting to show, in that table, which of the sites identified in the literature search were already annotated in ORegAnno and Pazar.
Finally, BLASTP was employed to check which of these predicted proteins were already annotated in the Homo sapiens, Bos taurus and Sus scrofa protein databases.
In the case of C. elegans many of the predicted exons are already annotated in Wormbase: 12 initial exons, 30 internal exons, and 13 3'-terminal exons.
(3) Moreover, DUF1636 and DUF2092 are already annotated in many genomes as a metal-binding protein and a periplasmic protein, respectively.
Another novelty of our study is that the training set was constructed to be substantially different from the set of genes that are already annotated in the GO database with some synapse-related GO term.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com