What is the UniProt ID?
The proteome identifier (UPID) is the unique identifier assigned to the set of proteins that constitute the proteome. It consists of the characters ‘UP’ followed by 9 digits, is stable across releases and can therefore be used to cite a UniProt proteome.
How do you retrieve a protein sequence 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.
Can you cite UniProt?
https://www.uniprot.org/uniparc/UPI00000002E4. Remarks: A UniProtKB accession number (AC) is a stable identifier and therefore allows unambiguous citation of a UniProtKB entry. This is not the case for the ‘Entry name’.
How do I find my Gene ID?
Some very good sources of gene IDs are the following websites:
- NCBI Gene – searches any provided ID, symbol or gene name across many databases. Strengths: ID conversion and free text lookup of gene names.
- SwissProt/UniProt – searches any provided ID or symbol.
- bioDBnet – similar to UniProt website.
How do I download files from UniProt?
UniProt is updated every eight weeks. 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 is UniProt of NCBI?
The UniProt Knowledgebase (UniProtKB) is an expertly curated database, a central access point for integrated protein information with cross-references to multiple sources. The UniProt Archive (UniParc) is a comprehensive sequence repository, reflecting the history of all protein sequences (1).
What is UniProt in bioinformatics?
The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. The UniProt databases are the UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters (UniRef), and the UniProt Archive (UniParc).
How do you find the nucleotide sequence in UniProt?
Select the Blast tab of the toolbar to run a sequence similarity search with the BLAST (Basic Local Alignment Search Tool) program:
- Enter either a protein or nucleotide sequence (raw sequence or fasta format) or a UniProt identifier into the form field.
- Click the Blast button.
How do I download a protein sequence?
- Open NCBI website (http://www.ncbi.nlm.nih.gov/)
- Select the Protein (ALL databases), write the name of protein.
- The list obtained, choice the specific protein click on that.
- Just below the name of the protein, FASTA is written, click on it.
- You get new page having full information of protein sequence for example :
How do you convert Entrez ID to gene symbol?
You can convert Entrez ID into gene name by using website called “MatchMiner” (http://discover.nci.nih.gov/matchminer/MatchMinerLookup.jsp). All you need to do is to upload a file that contains all your Entrez IDs. This website will convert them into HUGO gene names.
Can I use UniProt to map protein or gene data?
Although UniProt provides the retrieve id mapping function, it does not take into account the number of rows which means any protein or gene id which cannot be mapped is simply omitted from the output file. This makes combining the datasets difficult. There are numerous tools available for such kind of ID mapping.
Why can’t I use Uniprot ID’s as input to my application?
The struggle is more in case of UniProt id’s as very few applications accept them as input. Although UniProt provides the retrieve id mapping function, it does not take into account the number of rows which means any protein or gene id which cannot be mapped is simply omitted from the output file.
What is a gene name in UniProt?
They are IDs referred to as gene names and are used across a variety of databases including Uniprot. Note in section 2 of the ID mapping that I have set the left option to “gene name”. “STRING” won’t work. Show activity on this post. The first answer is good!
What is a gene name?
They are IDs referred to as gene names and are used across a variety of databases including Uniprot. Note in section 2 of the ID mapping that I have set the left option to “gene name”.