Sequence database setup: SwissProt
Overview
UniProtKB/Swiss-Prot (reviewed) is a high quality manually annotated and non-redundant protein sequence database, which brings together experimental results, computed features and scientific conclusions. About 85 % of the protein sequences in UniProtKB are derived from the translation of coding sequences (CDS) from the EMBL-Bank/GenBank/DDBJ public nucleic acid databases.UniProtKB is a collaboration between the European Bioinformatics Institute, the Swiss Institute of Bioinformatics and the Protein Information Resource.
Using the database in Mascot 2.5 and later
SwissProt is a predefined database, meaning up-to-date configuration information can be downloaded automatically by Database Manager. In Database Manager, from predefined definitions, choose SwissProt_ID to use the ID as the unique identifier or choose SwissProt_AC to use the AC. 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. We recommend updating 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.
UniProt:
https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/
EBI:
https://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase
The EBI site mirrors the UniProt site. The relevant files are:
- Version info: reldate.txt
- SwissProt Fasta file: uniprot_sprot.fasta.gz
- SwissProt Dat file: uniprot_sprot.dat.gz
Parse Rules
A typical SwissProt Fasta title line is:
>sp|Q4U9M9|104K_THEAN 104 kDa microneme/rhoptry antigen OS=Theileria annulata GN=TA08425 PE=3 SV=1
You can use either the ID (104K_THEAN) or the AC (Q4U9M9) as the identifier. Many people prefer the ID because it is semi-descriptive.
ID from Fasta title: ">..|[^|]*|\([^ ]*\)"
AC from Fasta title: ">..|\([^|]*\)"
Description from Fasta title: ">[^ ]* \(.*\)"
The corresponding lines in the Dat file are:
ID 104K_THEAN Reviewed; 893 AA. AC Q4U9M9;
ID from Ref file: "^ID \([^ ]*\)"
AC from Ref file: "^AC \([-A-Z0-9_]*\)"