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CGD Help: Genome Snapshot
This resource, which is updated daily, provides information on the
status of each genome in CGD. It includes information on the genomic features
and GO annotations. All the data displayed on this page are available
in one or more files (Chromosomal Feature File; GO Annotations File) on the CGD Download Data page. The Advanced Search tool can also
be used to retrieve chromosomal features that match specific criteria.
This pie chart shows the breakdown of the number of ORFs classified as
Verified, Uncharacterized, and
Dubious in the genome. ORFs are classified
"Uncharacterized", or "Dubious" by CGD according to
the degree of certainty that each ORF actually encodes a protein (see
the "ORF classification" section of the CGD Sequence
Documentation for details).
The Genome Inventory
table provides a count of each feature type
in the genome and in each chromosome. In addition, the table also
lists the size of the genome and of each chromosome. Clicking on any
of the feature types will provide a complete list of features of that type,
along with their coordinates and other details such as gene names and
descriptions. Only the feature types that are currently annotated in
the genome are listed in this table.
Note that there may be small differences between the total number of
each type of feature as shown in the Genome Inventory table, and as
derived from the Advanced Search. The number shown in the Genome
Inventory table includes only genomic features that are mapped to
chromosomes, while results from the Advanced Search tool may include
features that are not mapped to Assembly 21 chromosomes - for example,
genes of the MTLalpha locus, which are not included in Assembly 21
because it is a haploid assembly that includes the a mating
type allele of this locus. Additionally, the Genome Snapshot view
is updated once per day while the data in AspGD are updated multiple times per day.
This summary table provides the current total number of
gene products (protein and RNA gene products) that have been annotated
to one or more terms in each GO aspect (Biological Process, Molecular
Function and Cellular Component). Please note that these counts do not include the GO
annotations made for ORFs classified as "Dubious", or for features of
type "Pseudogene" or "Not physically mapped". Also
note that the number of annotations displayed in the "Total Number of
Annotations" column does not include annotations to the three terms
representing lack of knowledge at this time, i.e. "molecular_function
unknown", "biological_process unknown", or "cellular_component
unknown". The GO Annotations File available at CGD's Download Data page
provides the CGD GO annotations for download in bulk.
This section provides three bar graphs that represent the GO
annotation status of the entire genome using the Candida GO-Slim (a
high-level subset of Gene Ontology terms that allows grouping of genes
into broad categories such as "DNA replication", "protein kinase
activity", or "nucleus", tailored to Candida biology). GO-Slim terms
representing broad categories from a single aspect are listed for each
graph, along with the percentage of gene products
annotated to a specific term that maps up the ontology to the GO-Slim
term. Only the distribution of "known" Molecular Functions, Biological
Processes, and Cellular Components are included in these graphs;
annotations to "unknown" are excluded.
More information on GO and GO-Slim can be found at SGD's GO help page
or in the Gene Ontology documentation. The bar graphs are generated once a day.
The Genome Snapshot can be accessed via the following links: on CGD's home page under CGD Curation News; in the
left-hand sidebar of CGD's home page and other index pages, in
the "About CGD" section; and on the About CGD page.
Go to the Genome Snapshot
- CGD's Download Data page
- SGD's GO Help page
- Gene Ontology documentation