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All variations were mapped to all transcript models, which led to multiple annotations for several loci.
In the case of multiple annotations for a protein, maximum term similarity is taken as the protein similarity [ 32].
This returned a single annotation for 9,863 isogroups (43%), and multiple annotations for 199 isogroups that we excluded from further portions of this analysis.
However, the over-representation analysis at the functional level that we applied here allows multiple annotations for a single gene and, therefore, inherently overcomes this type of problems.
'Unknown' annotations are often present as the sole annotation for a GO aspect for a gene, but non-'unknown' annotations are typically part of a set containing multiple annotations for a gene.
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Also it is common, from a single article, to identify multiple annotations identified for one aspect and to annotate to different levels of granularity in the same branch of the ontology.
However, since we test each cluster for multiple annotations, a correction for multiple hypothesis is needed.
We believe that BEACON may help improve the quality of bacterial genome annotations deposited in public databases when multiple annotations are available for the same bacterial genome.
All genes with multiple annotations and four sequences for which neither a Genoscope annotation nor a DFCI match were found were removed from the data set, resulting in 2,359 unigenes.
Further, multiple annotation rings, for example depiction of gene copy number changes, can be uploaded as text files and represented as bar, histogram or heatmap rings.
Validation of the extracted modules by multiple annotation allows for the assessment of confidence measures assigned to the modules in a protein pathway context.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com