Universal Protein Resource (UniProt) ==================================== The Universal Protein Resource (UniProt), a collaboration between the European Bioinformatics Institute (EBI), the SIB Swiss Institute of Bioinformatics, and the Protein Information Resource (PIR), is comprised of three databases, each optimized for different uses. The UniProt Knowledgebase (UniProtKB) is the central access point for extensively curated protein information, including function, classification and cross-references. The UniProt Reference Clusters (UniRef) combine closely related sequences into a single record to speed up sequence similarity searches. The UniProt Archive (UniParc) is a comprehensive repository of all protein sequences, consisting only of unique identifiers and sequences. UniParc ======= The UniProt Archive (UniParc) is a non-redundant protein sequence archive, containing all new and revised protein sequences from all publicly available sources (http://www.uniprot.org/help/uniparc) to ensure that complete sequence coverage is available at a single site. To avoid redundancy, all sequences 100% identical over the entire length are merged, regardless of the source organism. New and updated sequences are cross-referenced to the source database accession number, and provided with a sequence version that increments upon changes to the underlying sequence. The basic information stored within each UniParc entry is the identifier, the sequence, cyclic redundancy check number, source database(s) with accession and version numbers, and a time stamp. In addition, each source database accession number is tagged with its status in that database, indicating if the sequence still exists or has been deleted in the source database and cross-references to NCBI GI and TaxId if appropriate. This directory contains the following: fasta/active/ Directory representing UniParc sequences with at least one active cross-reference to a source database, in gzip-compressed FASTA format. The data has been split into smaller files for more robust downloads. All files from this directory need to be downloaded and combined. xml/all/ Directory containing all UniParc sequences, including those that have been deleted from the source database in XML format, split into smaller files. All files from this directory need to be downloaded and combined. The XML files include: - cross-references to the source databases - status of the sequence in each source database (e.g. if the sequence still exists, the status will be "active") - source database accession numbers and version - cross-references to NCBI GI and TaxID if appropriate uniparc.xsd Schema definition for the UniParc XML format. Related files can be found in xml/all directory This file and directories are updated with each UniProt release. File names might be unchanged, but data is likely to be different or start at different offsets. We therefore strongly recommend to download the full set. Please note: From UniProt release 2023_02 onwards we are no longer providing the full uniparc_active.fasta.gz and uniparc_all.xml.gz files. The size of these files had grown over the years to more than 100 and 200 Gigabytes, respectively, which made them difficult to download. We now therefore split these files into sets of smaller files. FTP geographical sites Switzerland https://ftp.expasy.org/databases/uniprot/current_release/uniparc United Kingdom https://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/uniparc USA https://ftp.uniprot.org/pub/databases/uniprot/current_release/uniparc Example wget command line to get all fasta files using Switzerland's FTP: wget -r -nd --no-parent -A 'uniparc_active_p*.fasta.gz' https://ftp.expasy.org/databases/uniprot/current_release/uniparc/fasta/active -e robots=off -------------------------------------------------------------------------------- LICENSE -------------------------------------------------------------------------------- We have chosen to apply the Creative Commons Attribution 4.0 International (CC BY 4.0) License (https://creativecommons.org/licenses/by/4.0/) to all copyrightable parts of our databases. (c) 2002-2024 UniProt Consortium -------------------------------------------------------------------------------- DISCLAIMER -------------------------------------------------------------------------------- We make no warranties regarding the correctness of the data, and disclaim liability for damages resulting from its use. We cannot provide unrestricted permission regarding the use of the data, as some data may be covered by patents or other rights. Any medical or genetic information is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.