Sequence database setup: UniProt proteomes
A UniProt complete proteome consists of the set of proteins thought to be expressed by an organism whose genome has been completely sequenced. A reference proteome is the complete proteome of a representative, well-studied model organism or an organism of interest for biomedical research.
UniProtKB is a collaboration between the European Bioinformatics Institute, the Swiss Institute of Bioinformatics and the Protein Information Resource.
This guide is also available on Youtube: Mascot Server: Setting up a Uniprot proteome database.
Proteome ID
First, you need to discover the Proteome ID for your proteome of interest by searching https://www.uniprot.org/proteomes/. This example uses rice, taxonomy Oryza sativa subsp. japonica with Proteome ID UP000059680.
Create the database
In Database Manager, create a new custom definition, as follows:
- FASTA, New database; Create New
- Use pre-defined template; UniProt_proteome_template
- Next, Create
- Download from remote URL; Next
- Set up download URL
- Paste the following into the FASTA file URL field, where the proteome ID is for your proteome of interest
https://rest.uniprot.org/uniprotkb/stream?query=proteome:UP000059680&format=fasta&compressed=false&includeIsoform=true - Save; Start downloading
- Activate
Once configured, you can enable automatic updating by clicking on the database name then choosing Edit schedule.
Example configuration
