These are tracked as Prospective CCDS cases in the internal website with a mechanism for curators to flag annotations that can readily be added to the CCDS data set based on an annotation addition or update by RefSeq or HAVANA.
To differentiate annotations generated with our software from manually generated tags, we flag the annotations with the 'IEA' evidence code (Inferred by Electronic Annotation) taken from the Gene Ontology (Ashburner et al., 2000).
A note annotation flag appears as a small pad-and-pen icon.
On the list of current annotations, the green flag denoting that an annotation has changed in the last seven days should be placed next to the checkbox instead of at the end of the line.
Genes flagged by 'mismatch' annotation pair discrepancies could be updated 59.2% (157/265) of the time, while 78.8% (208/264) of genes flagged by 'shallow' annotation pair discrepancies could be updated.
We generated checkboxes for all the FlyBase triage flags, so the annotation of the tagtog corpus could be used directly in the FlyBase curation.
The curator first performed automated checks on the GFF3 and FASTA coding sequences to flag potential conflicting annotations and coding sequences that have stop codons for further inspection and revision.
Exons smaller than 20 codons are difficult to identify by BLAST, so if a pillar that generates a hit contains a small exon, only the larger exon(s) are usually detected in a TBLASTN search, and therefore the hit is flagged for manual annotation.
Thus, the reported genome includes a single copy of the repeating motif flagged with a repeat annotation.
The microarray data, including median foreground and background intensities, flags and feature annotations, were imported into R/Bioconductor.
Additionally, CAVA flagged that alternative annotations were possible for 34 mutations, though none altered the class (i.e., all possible representations result in a frameshift).
