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The manual GENCODE annotations for Ensembl annotation are probably the most reliable annotation of human protein-coding genes.
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The most reliable annotations are those inferred directly from experimental evidence.
All data goes through a review process where only the most reliable annotations are kept to reduce noise in the system.
Usually, the most reliable functional annotations for metagenomic sequences are achieved using homology-based approaches against publicly available reference sequence databases.
For analysis on the Exon Array, we only used core probe sets that are supported by the most reliable and accurate annotation.
This set of parameters was shown to provide the most reliable results in the annotation of Arabidopsis sequences [ 38].
When possible, we assigned the ID to the UniProtKB that provides the most reliable sequence information and annotations.
Using these three methods, reliable annotation for most differentially regulated genes was obtained.
Manual annotation is considered to be the most reliable method of producing a high quality genome annotation, but this is time consuming and can be a bottleneck in genome studies [ 34].
Given these difficulties, experimental discovery and annotation remains the most reliable method for TFBS discovery; however, such validation is often unavailable for individual TFs.
With respect to the dual 3'Seq approach a multi-step annotation procedure was employed to ensure the most reliable assignment of reads to the corresponding transcript.
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