ID Mapper


The ID Mapper tool maps PATRIC identifiers to those from other prominent external databases such as GenBank, RefSeq, EMBL, UniProt, KEGG, etc. Alternatively, it can map a list of external database identifiers to the corresponding PATRIC features.

ID Mapping Sources

  • First, PATRIC CDSs (protein coding genes) are mapped to corresponding CDSs in RefSeq/GenBank by matching their stop position on genome sequences.
  • Second, RefSeq/GenBank CDSs are mapped to corresponding UniProtKB Accession.
  • Third, mappings are extended to other prominent external database identifiers using UniProt’s ID Mapping Service.

PATRIC <-> RefSeq/GenBank <-> UniProtKB Accession <-> Other External Databases

Using the ID Mapper Tool

The ID Mapper submenu option under the Services main menu (Data category) opens the ID Mapper input form (shown below). Note: You must be logged into PATRIC to use this tool.

../../_images/services_menu.pngID Mapper Menu


../../_images/id_mapper_input_form.pngID Mapper Input Form

From: Dropdown list for electing which ID type (PATRIC, RefSeq, Uniprot-KB, etc.) to map from (source).

To: Dropdown list for selecting which ID type (PATRIC, RefSeq, Uniprot-KB, etc.) to map to (target).

IDs: Input box for specifying the IDs to map. The IDs can be specified in a comma-separated or one-per-line list.

PATRIC Feature Strategy

This tool uses the Uniprot-KB mapping table to map external IDs to PATRIC. This is done using NCBI IDs. Due to updates over time some NCBI IDs may achieve better mapping results than others.


Map: Launches the mapping service, which, upon completion, displays a table below it containing all the matching items (e.g., features, genomes, etc.) that map to the list of IDs provided.