Mascot: The trusted reference standard for protein identification by mass spectrometry for 25 years

Sequence database setup: UniRef

Overview

UniRef (UniProt Reference Clusters) provide clustered sets of sequences from the UniProt Knowledgebase (including isoforms). The seed sequences are the longest members of the cluster.

There are three versions of UniRef: UniRef100, UniRef90, and UniRef50. UniRef100 is non-identical, while UniRef90 and UniRef50 are non-redundant at a sequence similarity level of 90% and 50% respectively. Searching with mass spectrometry data requires the exact sequence to be present in the database, so UniRef100 is the version to choose.

Using the database in Mascot 2.5 and later

UniRef100 is a predefined database, meaning up-to-date configuration information can be downloaded automatically by Database Manager. In Database Manager, choose UniRef100 under predefined definitions. Database Manager will download the up-to-date configuration information and the sequence database files.

Using the database in Mascot 2.4

Mascot Server 2.4 does not support HTTPS file downloads. Please update to a later version of Mascot Server.

Using the database in Mascot 2.3 and earlier

Please refer to the local copy of this help page shipped with your version of Mascot Server.

Download URLs

The URLs are provided here for reference. If you are using Database Manager, you do not need to manually download these files.

EBI: https://ftp.ebi.ac.uk/pub/databases/uniprot/uniref/uniref100/
UniProt: https://ftp.uniprot.org/pub/databases/uniprot/current_release/uniref/uniref100/

The files are:

  • Version info: uniref100.release_note
  • Fasta file: uniref100.fasta.gz

Note that the XML file, uniref100.xml.gz, contains essentially the same information as the Fasta file. It is not a full text reference file.

Parse Rules

A typical UniRef Fasta title line is:

>UniRef100_Q4U9M9 104 kDa microneme/rhoptry antigen n=1 Tax=Theileria annulata RepID=104K_THEAN

The literal text, UniRef100_, should be dropped from the accession string, to make linking easier.

Accession from Fasta title: ">UniRef100_\([^ ]*\)"
Description from Fasta title: ">[^ ]* \(.*\)"