How do I access UniProt?
Navigating the UniProt tools
- The Basic Local Alignment Search Tool (BLAST) for sequence search.
- the ‘Align’ multiple sequence alignment tool.
- the ‘Retrieve/ID Mapping’ tool where you can submit a list of identifiers to retrieve the corresponding UniProt entries, or map them from or to an external database.
What is a UniProt entry?
UniProtKB/TrEMBL entry names The UniProtKB/TrEMBL entry name consists of up to 16 uppercase alphanumeric characters with a naming convention similar to that of UniProtKB/Swiss-Prot, where: Y is a mnemonic species identification code of at most 5 alphanumeric characters.
How do I download from UniProt?
You can download small data sets and subsets directly from this website by following the download link on any search result page. For downloading complete data sets we recommend using ftp.uniprot.org.
What APIs are widely used for programmatic access to XML data?
UniProt provides several application programming interfaces (APIs) to query and access its data programmatically:
- UniProt website REST API.
- Proteins REST API.
- UniProt SPARQL API.
- UniProt Java API.
What is the difference between version number and GI number?
The version number (U49845. 1) and GI (1293613) are unique identifiers for the sequence data within a record. If any change occurs to the sequence data, no matter how large or small, the version number for that sequence is incremented by one decimal and a new GI number is assigned.
How do I retrieve data from UniProt?
Retrieving sequences from the website
- Perform your favorite query and view the resulting list of entries (e.g. this query retrieves all UniProtKB entries that are part of the human proteome: proteome:UP000005640)
- Click the Download button in the query result page.
Is UniProt a primary database?
UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects….UniProt.
| Content | |
|---|---|
| Primary citation | UniProt Consortium |
| Access | |
| Data format | Custom flat file, FASTA, GFF, RDF, XML. |
| Website | www.uniprot.org www.uniprot.org/news/ |
What is the difference between Swiss-Prot and TrEMBL?
TrEMBL is a computer-annotated supplement of SWISS-PROT that contains all the translations of EMBL nucleotide sequence entries, which are not yet integrated in SWISS-PROT. Currently, SWISS-PROT and TrEMBL have 0.5 and 7.6 million sequences, respectively.
What is the mission of the UniProt project?
The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. Manually annotated and reviewed. Records with information extracted from literature and curator-evaluated computational analysis.
How to cite us in the UniProt consortium?
How to cite us The UniProt Consortium Submit your data Submit your sequences, publications and annotation updates Programmatic access Query UniProt data using APIs providing REST, SPARQL and Java services
Is the UniProt database redundant or non redundant?
The UniProt Reference Clusters (UniRef) provide clustered sets of sequences from the UniProt Knowledgebase (including isoforms) and selected UniParc records. UniParc is a comprehensive and non-redundant database that contains most of the publicly available protein sequences in the world.
What’s the purpose of the UniProt protein basket?
When browsing through different UniProt proteins, you can use the ‘basket’ to save them, so that you can back to find or analyse them later. More… The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information.