Genome Finder Overview
The Genome Finder allows you to locate genomes within PATRIC based on genome names and/or associated genome metadata. To learn about various types of available genome metadata, see Genome Metadata FAQs.
Accessing Genome Finder on the PATRIC site
An advanced search, described below, may be conducted by selecting “Genome Finder” from the “Searches and Tools” tab in the main navigation along the top of the PATRIC site or 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 the Genome Finder from the “Search Tools” box on an Organism Landing page will be pre-scoped to the taxonomic level of the page.
Using Genome Finder
You may locate genomes by 1) selecting organisms and/or 2) entering a keyword.
- To select organisms, locate 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.
- To search based on available genome metadata, enter a keyword, or series of keywords, into the keyword text box. If no keyword attribute is chosen from the keyword dropdown menu, then the search will include all 61 metadata attribute fields. For a complete list of attributes, see Genome Metadata FAQs.
Once your search parameters are selected, click on the Search button. You will be taken to a Genome Finder results table, where results may be viewed via the default Genomes tab or the Sequences tab. Note: Larger searches may take PATRIC several minutes.
Genome Finder Results Table
- All tables accessed via the Genome Finder may be sorted as described in Feature Table FAQs.
- Filter controls along the left allow you to filter the data based on six key metadata attributes (in orange text), Genome Status, Isolation Country, Host name, Disease, Collection data, and Completion date. To see all of the information associated with a specific attribute in the list, click the “more” buttons, located within the list.
- From the Genomes tab you can navigate within rows to specific PATRIC Organism Landing pages (Organism Name), genome browser illustrations of a specific feature within the context of it’s genome (Genome Browser ), specific PATRIC feature tables containing sequences (Sequences) or specific sets of CoDing Sequences (CDS columns). For more information on the Genome Browser, see Genome Browser FAQs.
- From the Sequences tab you can navigate within rows to specific PATRIC Genome Landing pages (Genome Name), NCBI nucleotide pages for that genome (Accession), genome browser illustrations of a specific feature within the context of its genome (Genome Browser ), and other data. For more information on the Genome Browser, see Genome Browser FAQs.
- From either tab, you may utilize the Genome Finder Table Toolbar, located in the light blue row to:
- Save selected genomes to groups within your Workspace by clicking the Add Genomes(s) button. To learn more about how to save data for future visits and utilize your personal Workspace see Workspace FAQs.
- Download data as an Excel or txt file. Note: The table will be downloaded in its entirety (all 61 attributes) regardless of which columns are currently being shown/hidden.
- Customize which of the 61 metadata columns are shown/hidden in your results table with the Columns button. For a complete list of attributes, see Genome Metadata FAQs.
- Access the PATRIC FAQs glossary within PATRIC eNews by clicking on the “PATRIC FAQs” Help button.
To learn about what Metadata is available, how to access it via routes other than the Genome Finder, and Metadata sources see Genome Metadata FAQs.