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The YLS-specific genes were annotated mainly for metabolic processes (starch and sucrose metabolism, purine metabolism and cyanoamino acid metabolism, etc).
These results are clearly biased towards organisms whose genome has been largely and deeply studied and annotated, mainly because of the higher quality of genome assemblies, of the more accurate gene predictions and of the higher number of protein sequences deposited in public sequence databases.
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Annotation of 46 bacterial and archea genomes using this approach has shown that purely bioinformatics-based pipelines fail to annotate mainly short-length proteins and high G + C content sequences [ 15].
The path analysis on the EndoNet webpage outputs all shortest paths between two nodes independent of any circumstances, whereas the manually annotated pathways (mainly endocrine axes) are limited in number and restricted to already known pathways.
It is mainly annotated for linguistic structures such POS tagging and syntax annotation, semantic annotation of entities and so on [25, 26].
They are mainly annotated as being involved in the response to infection, as well as in cell motility and cytoskeleton remodelling (Figure 2).
Of note, most of the above so far in-depth studied genes, regardless whether EWS-FLI1 up- or down-regulated, are mainly annotated to be involved in signaling, morphogenesis, development and other more specialized functions.
These genes were mainly annotated as being related to the development of the nervous system, including NCAM2, Neurexin1, doublecortin, neurofascin, synaptotagmins and synapsins to list a few, which affect both the structure and the function of the nervous system.
For each of these three ontologies, annotated sequences are mainly distributed among two or three of the general term categories.
Traditionally coding genes (tRNAs, rRNAs) were mainly annotated using automated pipelines 22 and noncoding sRNA regions were overlooked for the past fifty years.
Genes with decreased expression in both LS and HS families were mainly annotated to functional categories associated with protein complex assembly and translation.
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