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.

Graphical View of Protein Coding Genes

This pie chart shows the breakdown of the number of ORFs classified as Verified, Uncharacterized, and Dubious in the genome. ORFs are classified as "Verified", "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).

Genome Inventory

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.

Summary of GO annotations

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.

Distribution of Gene Products by Process, Function and Component

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.

Accessing the Genome Snapshot

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.

Other Relevant Links

  1. Advanced Search Tool
  2. CGD's Download Data page
  3. SGD's GO Help page
  4. Gene Ontology documentation page
Go to the Genome Snapshot

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