SGD Help: Genome Snapshot

View a quick video tutorial about SGD's Genome Snapshot.

Contents

1. Description
2. Genome Inventory
3. Summary of GO Annotations
4. Summary of Phenotype Annotations
5. Accessing the Genome Snapshot

Description

The Genome Snapshot provides information on the annotation status of the Saccharomyces cerevisiae genome. It includes information on the genomic features, Gene Ontology (GO) annotations, and Phenotype annotations. All the data displayed on this page are available in one or more files (SGD_features.tab, gene_associations.sgd, go_slim_mapping.tab, phenotype_data.tab) at SGD's Downloads site. YeastMine can also be used to retrieve chromosomal features that match specific criteria.

Genome Inventory

The Genome Inventory provides counts of each type of feature in the genome and on each chromosome. ORFs are classified as "Verified", "Uncharacterized", or "Dubious" according to the degree of certainty that each ORF actually encodes a protein. Definitions for each feature type can be found in the Glossary. On the bar graph, mouseover each bar or label to see the count. The table view also lists the size of the nuclear and mitochondrial genomes, and of each chromosome. In both the graph and table, clicking on any of the feature type labels will provide a complete list of loci of that type.

Summary of GO Annotations

This section provides three bar graphs that represent the GO annotation status of the entire genome using the yeast 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 yeast biology. GO-Slim terms representing broad categories from a single aspect are listed for each graph, along with the number of S. cerevisiae gene products annotated to a specific term that maps up the ontology to the GO-Slim term. The complete mapping approach, which maps features to all available GO Slim terms, is used to generate the bar graphs. Annotations to the three terms representing lack of knowledge at this time, i.e. "molecular_function unknown", "biological_process unknown", or "cellular_component unknown" are listed as 'annotated to unknown'. Only annotations made by manually curated and high-throughput methods are included. 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 in S288C". More information on GO and GO-Slim can be found in SGD's GO help page. The data summarized in these graphs is available in the go_slim_mapping.tab file, on SGD's Downloads site. The data are updated weekly.

Summary of Phenotype Annotations

This bar graph represents the state of phenotype annotations for the entire S. cerevisiae genome using a phenotype slim (i.e., a high-level subset of phenotype terms that allows grouping of phenotypes into broad categories such as "lifespan", "stress resistance", and "cellular morphology"). More information about phenotype annotation and the ontology can be found on SGD’s phenotype help page. All the phenotype data summarized on this graph can be found in the phenotype_data.tab file at SGD's Downloads site. The data are updated daily.

Accessing the Genome Snapshot

The Genome Snapshot can be accessed via the Reference Genome option on the Sequence pull down menu in the purple toolbar traversing the top of most SGD webpages.

Go to the Genome Snapshot