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.
ID Mapper Menu
ID 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.