Search AgBase
The AgBase text search allows you to search through all entries in the AgBase database (or a subset of the database) to find entries of interest. You can search by protein names, by gene name, both protein name and gene name, or GO term.
Select AgBase Database: use this drop down menu to narrow your search to particular species. If the species you are interested in is not listed, please use the default setting to search all of AgBase. Note that the AgBase database contains all GO annotations, not just annotations for those species listed. You may request that your species of interest is added to the AgBase species pages by contacting AgBase directly.
Browse by: The AgBase Text Search allows you to search by Name Type or ID Type.
Name Type: users may specify searching for a protein name, gene name, protein or gene name or GO Term name. The default search is to find exact matches. However, very few agriculturally important species have standardized gene nomenclature projects and searching for names can be complicated. Currently, Protein Name searches names for UniProt records while Gene Name searches for the equivalent Entrez Gene names. Protein/Gene Name will search either.
To facilitate searching we provide options for the user to include synonym matches and wildcard matches. Selecting synonym matches will also search for other known names or aliases for the name. For example, the CD30 antigen is more correctly known as tumor necrosis factor receptor superfamily, member 8 (gene symbol: TNFRSF8). Doing a Gene Name search of the AgBase chicken database for CD30 without selecting synonym and wildcard matches does not return any answers because CD30 is a synonym, not a recognized gene symbol or name. If the search is repeated with the synonym matches selected, the correct record is returned (UniProtKB record Q800I0). Selecting wildcard matches will search for matches with the entry included as part of the name. For example a wildcard match for TNFR will return all TNFR family records (e.g. TNFRSF1B, TNFRSF8, TNFRSF11B, etc).
ID Type: Users may search for UniProtKB IDs or accessions, Genbank accessions or gi numbers, GO term IDs.
In addition we include "ID Not Specified". The ID Not Specified option allows users to enter a mixed list of any of the other supported IDs.
To facilitate searching we provide options for the user to include synonym matches and wildcard matches. Selecting synonym matches will also search for other known names or aliases for the name. For example, the CD30 antigen is more correctly known as tumor necrosis factor receptor superfamily, member 8 (gene symbol: TNFRSF8). Doing a Gene Name search of the AgBase chicken database for CD30 without selecting synonym and wildcard matches does not return any answers because CD30 is a synonym, not a recognized gene symbol or name. If the search is repeated with the synonym matches selected, the correct record is returned (UniProtKB record Q800I0). Selecting wildcard matches will search for matches with the entry included as part of the name. For example a wildcard match for TNFR will return all TNFR family records (e.g. TNFRSF1B, TNFRSF8, TNFRSF11B, etc).
ID Type: Users may search for UniProtKB IDs or accessions, Genbank accessions or gi numbers, GO term IDs.
In addition we include "ID Not Specified". The ID Not Specified option allows users to enter a mixed list of any of the other supported IDs.
Multiple Queries: users may enter more than one search term by separating the term with a return or new line.
Results: The text search returns a table containing the matches is displayed, and each Accession links to the Entry Detail page, containing Name and Organism information, Sequence Information, Database Cross-References, and GO Annotations.
This search interface is designed for simple text searches. To find longer lists of accessions for gene modeling, we recommend the use of the GORetriever tool. To see all the proteins associated for a species, please use GOProfiler. The "Number of annotated gene products link" and the "Number of unannotated gene products link" will provide a complete list of gene products associated with a taxon.
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