Accessing the Download Data Tool on the PATRIC Website
The Download Data Tool may be accessed via the Downloads tab at the top of any PATRIC page. Alternatively, it may be accessed by clicking “Download genome data” in the upper-right of any PATRIC Organism Landing page. Note: The “Download genome data” button will give you taxonomy table options for the taxon level of the Organism Landing page you start from.
Using the Download Data Tool
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. Next specify one or more Annotation Sources, select File Types, and click on the “Download” button. For an explanation of various annotation sources, please see Annotation FAQs.
Note for Windows Users: Data are downloaded as a zip file (patric_downloads.zip). If double clicking on this zip file gives the appearance that the file is empty, please extract the files in one of the two following ways:
- Right click on the downloaded zip file and select “Extract files…” or “Extract Here” from the menu.
- If you have 7-Zip: Right click on the downloaded zip file and select 7-Zip from the menu. Then select “Extract files…” or “Extract Here”.
Supported File Types
*.fna: genomic sequences in FASTA format
*.ffn: DNA sequences of protein coding genes in FASTA format
*.frn: DNA sequences of RNA coding genes in FASTA format
*.faa: protein sequences in FASTA format
*.gbf: all annotations in GenBank file format
*.features.tab: all genomic features in tab-delimited format
*.cds.tab: protein coding genes in tab-delimited format
*.rna.tab: RNAs in tab-delimited format
*.go: GO function assignments in tab-delimited format
*.ec EC: assignments in tab-delimited format
*.path: pathway assignments in tab-delimited format
*.PATRIC.*: Annotations by PATRIC/RAST system
*.RefSeq.*: Annotations by RefSeq / GenBank
*.BRC.*: Annotations by Legacy BRC
*.PATRIC2RefSeq.tab: Mappings between PATRIC and RefSeq annotated features