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Of the 336 genes that were reviewed, ∼77% required an update to the annotation set, ranging from a refinement of an annotation, removal of an annotation or an addition of a new annotation.
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Furthermore, PATRIC offers continued updates to the annotation of rickettsial genes and proteins, and provides multiple sequence alignments as well as phylogenetic trees, when applicable, for each OG consisting of two to ten rickettsial taxa.
The rich breadth of our functional data allowed us to make significant updates to the annotation of the C. difficile 630 reference genome.
A table containing updates to the annotation of these sequences will be available at the Laboratory of Mammalian Genome Biology website [ 68].
Since then, our understanding of the Arabidopsis genome structure and transcriptome has been improved through the release of 4 sequential updates to the annotation, culminating in The Institute for Genomic Research's release 5 (TIGR5), which forms the basis of the work presented here.
After TIGR's fifth and final release, Arabidopsis annotation responsibility was transferred to TAIR who have recently released an update to the Arabidopsis annotation (TAIR6).
Both of these situations necessitate an update to the genome annotation.
In addition, we also made available the list of SNPs underlying the probe hybridization sequences as an update to the Illumina annotation.
Genes in both of these classes were reviewed, since the computational predictions provided additional or different information from the existing manual annotations, suggesting that updates to the manual annotations might be necessary.
We thus performed an update according to the annotation pipeline described for the ITS2 database [ 29, 30].
Given the many changes and updates to the ontologies and annotations described here, no single annotation file can be considered as definitive.
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