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The sequences of a total of 13 BAC clones spanning the S H 3 locus in three coffee genomes (i.e. Ea and Ca sub-genome from C. arabica and Cc from C. canephora), were examined for the presence of R-genes using the previously determined annotation [ 48].
However, enrichment analysis of an independent set of experimentally determined annotations, the MGI mouse phenotypes, highlighted the same biological processes, thus validating the GO results.
We have compared the GO term enrichment of proteins with experimentally determined annotations obtained at the start of the initiative with annotations currently available.
The community lacks a generic measure for determining annotation quality and correctness, which we look at addressing within this article.
All of these approaches rely upon additional information to determine annotation quality.
It can help researchers determine annotation sample size for supervised machine learning.
The NCBI database Gene [ 10] was used to determine annotations for the rhesus draft genome.
Genomes were also compared for the presence or absence of Pfam domain annotations to determine annotations that are specific to one or two of the six completely sequenced strains of R. palustris.
Taxa of the contigs were determined by annotation of the best hit.
** For a junction read, the strand of the RNA is determined by the annotation if the junction is annotated, or by the splice signal if it's a novel junction.
The fold change at the gene level was obtained by averaging the fold change ratios of all transcripts belonging to the same gene, as determined by annotation using blastp [ 36].
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