Accessing GO Search on the PATRIC Website
An advanced search, described below, may be conducted from the “Searches and Tools” tab at the top of the PATRIC site and from the “Search Tools” box on any Organism Landing page. To learn about Organism Landing pages, see the PATRIC Data Organization Overview tutorial.
- Note: Searches conducted using EC Search from the “Search Tools” box on an Organism Landing page will be pre-scoped to the taxonomic level of the page.
GO Search Overview
The Gene Ontology (GO) project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases.? The ontology covers three domains: cellular component, molecular function, and biological process. For more information, please visit the Gene Ontology website. Our GO Search tool enables researchers to locate proteins annotated with specified GO criteria.
Using GO Search
To begin, select your phylum, class, order, family, genus, species, or genomes of interest via the Taxonomy Tree tab, the Alphabetized Organism tab, or begin typing in the “Jump to” field. Additionally, if you are a registered PATRIC user, you may access any saved organism data via the My Groups tab. You may also chose to filter your search via entering a Keyword, GO Term ID, GO Term Description, or Annotation Source. Then click on the Search button. You will be taken to an initial GO Search Results Table. Note: Larger searches may take PATRIC several minutes.
GO Search Results Table
- All tables accessed via GO Search may be sorted as described in Feature Table FAQs.
- Search results may be filtered by keyword or various Metadata categories, such as Annotation using the “Filter By” panel on the left. For an explanation of various annotation sources, see Annotation FAQs.
- You may click on links in the GO Search Results Table within rows to navigate to specific PATRIC genome pages (Genome Name), NCBI nucleotide page for that genome (Accession), specific PATRIC locus pages (Locus Tag), the Gene Ontology page for a specific GO Term (GO Term ID). Note: The Accession column in not shown in the default view. For information on what you may do from a PATRIC Pathways Table see Comparative Pathway Tool FAQs.
- You may utilize the GO Search Table Toolbar, located in the light blue row to:
- Save selected items to groups within your Workspace by clicking the Add Feature(s) button. To learn more about how to save data for future visits and utilize your personal Workspace please see Workspace FAQs.
- View or download selected DNA and/or protein sequence data in FASTA format. The table itself, or selected data within it, are also downloadable in both excel and .txt file formats.
- View pathways and associated pathway information for your selected genes by clicking the Pathway Summary button.
- Conduct Multiple Sequence Alignment analysis on selected items by clicking the Multiple Sequence Alignment button. For more details on this tool please see Multiple Sequence Alignment FAQs.
- Utilize the ID Mapping Tool on selected items by clicking the Map IDs Tools button. For more information on this tool please see ID Mapping FAQs.
- Customize columns shown/hidden in your results table with the Columns button.
- Access the PATRIC FAQs glossary within PATRIC eNews by clicking on the PATRIC FAQs Help button.