What is the UniProt ID?

Last modified April 10, 2018. 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 I find my UniProt ID?

Select the Retrieve/ID mapping tab of the toolbar and enter or upload a list of identifiers (or gene names) to do one of the following: Retrieve the corresponding UniProt entries to download them or work with them on this website.

How do I get my UniProt ID from NCBI?

Go the UniProt home page at http://www.uniprot.org/.

1. Click on the ‘Retrieve/ID Mapping’ link, which is available in the header bar on all UniProt pages as shown in Figure 1.
2. You will see the ‘Retrieve/ID Mapping’ input page as shown in Figure 12.

What is UniProt KB database?

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.

How does UniProt do Geneid and RefSeq mappings?

How does UniProt do GeneID and RefSeq mappings? As per a protocol we have formalized with the NCBI, we create a RefSeq protein-centric mapping. If a UniProtKB protein (canonical or isoform sequence) then that RefSeq accession is mapped to the UniProtKB protein and consequently the entry will also get the corresponding GeneID cross-reference.

Can you submit an identifier in UniProt?

When mapping from a source database external to UniProt, you can submit any identifier as used in the UniProtKB cross-references . If your job is not successful and you are not sure which source database to use, try a text search in UniProtKB with one of your identifiers, and look at an example entry.

How often does the UniProt data set get updated?

UniProt is updated every eight weeks (see FAQ on how to be notified automatically of updates ). You can download small data sets and subsets directly from this website by following the download link on any search result page.

How are sequence database identifiers mapped to UniProtKB?

When mapping popular sequence database identifiers such as RefSeq, gi numbers, EMBL, EMBLCDS to UniProtKB, unmapped identifiers can be further mapped to UniParc. This can be particularly useful for proteins from redundant proteomes. Very large mapping requests (>50,000 identifiers) are likely to fail.

What is a gene ID?

Gene ID is a stable ID for that particular locus in that organism. (remains the same even if info about the locus changes such as gene symbol, genomic position, etc.) Official gene symbol and which organization provided it. Aliases/alternative symbols by which the gene might have been know in earlier times.

How do you get Entrez Gene ID?

The information in Entrez Gene can be accessed in multiple ways at NCBI (Table 2). The most direct is to submit a query to Entrez from the NCBI home page and display the results in Gene, or enter a query in any Entrez query bar and restrict the database search to Gene.

What is the E value in blast?

The Expect value (E) is a parameter that describes the number of hits one can “expect” to see by chance when searching a database of a particular size. It decreases exponentially as the Score (S) of the match increases. Essentially, the E value describes the random background noise.

What is the difference between id and AC number in swissprot entry?

Accession numbers are stable from release to release. If several UniProtKB entries are merged into one, for reasons of minimizing redundancy, the accession numbers of all relevant entries are kept. However, an accession number (AC) is always conserved, and therefore allows unambiguous citation of UniProt entries.

What does a gene code for?

Genetic code, the sequence of nucleotides in deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) that determines the amino acid sequence of proteins. Instead, a messenger RNA (mRNA) molecule is synthesized from the DNA and directs the formation of the protein.

What is UniProt number?

These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’. UniProtKB accession numbers consist of 6 or 10 alphanumerical characters in the format: 1. 2.

How do you get a gene in NCBI?

From the NCBI home page, click on the Search pull-down menu to select the Gene database, type the Gene Name in the text box and click Go. See Gene Help for tips searching Gene. Locate the desired Gene record in the results and click the symbol to open the record.

How to make a gene ID conversion tool?

Do More… The tool was made possible with the help of mygene.info API. Please visit mygene.info/v2/api/ for bulk queries. Also you can download python package from https://pypi.python.org/pypi/mygene .

How is Abid used in Gene ID conversion?

More information about the methodology, design, and possible use cases of ABID can be found in the documentation. ABID allows conversion by identifier, genomic interval, and DNA sequence. For more information about why ABID improves on other ID conversion tools, please see our paper in BMC Bioinformatics .

Where do I find converted Gene IDs in David?

Click on big button on the top of right panel. It will bring back to DAVID for other analytical tools. You also find the gene IDs just converted automatically appear as a new gene list in DAVID Gene List manager. 5. Terminology For “Conversion Summary” Table

How to convert fbgn IDs to gene symbols?

FlyBase ID Converter This tool will convert gene symbols, annotation IDs ( CG numbers ), refSeq IDs ( NM_ NR_ numbers ) to current Flybase IDs ( FBgn number ) and vice-versa. Paste in your list of gene symbols, annotation IDs, refSeq IDs or FBgn IDs and convert!