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Most Ensembl Genomes data is stored in MySQL relational databases and can be accessed by the Ensembl REST interface, the Perl API, Biomart or online. [5] Ensembl Genomes is an open project, and most of the code, tools, and data are available to the public. [6] Ensembl and Ensembl Genomes software uses an Apache 2.0 license [7] license.
Upon doing this, they can post a gene by gene symbol, Entrez ID or Ensembl gene ID. They can also specify genes by OMIM number or genomic location. If an identical gene has already been posted by another user, the match is made immediately and both users receive an email with the contact details of the other user.
[1] [5] [6] The GeneCards database provides access to free Web resources about more than 350,000 known and predicted human genes, integrated from >150 data resources, such as HGNC, Ensembl, and NCBI. The core gene list is based on NCBI, Ensembl and approved gene symbols published by the HUGO Gene Nomenclature Committee (HGNC).
Ensembl makes these data freely accessible to the world research community. All the data and code produced by the Ensembl project is available to download, [7] and there is also a publicly accessible database server allowing remote access. In addition, the Ensembl website provides computer-generated visual displays of much of the data.
The European Nucleotide Archive (ENA) is a repository providing free and unrestricted access to annotated DNA and RNA sequences.It also stores complementary information such as experimental procedures, details of sequence assembly and other metadata related to sequencing projects. [1]
In cases of allelic heterogeneity, the MIM number of the entry is followed by a decimal point and a unique 4-digit number specifying the variant. [9] For example, allelic variants in the HBB gene (141900) are numbered 141900.0001 through 141900.0538. [10]
Users can select various types of identifiers such as CCDS ID, gene ID, gene symbol, nucleotide ID and protein ID to search for specific CCDS information. [1] The CCDS reports (Figure 1) are presented in a table format, providing links to specific resources, such as a history report, Entrez Gene [ 10 ] or re-query the CCDS data set.
The GenBank release notes for release 250.0 (June 2022) state that "from 1982 to the present, the number of bases in GenBank has doubled approximately every 18 months". [ 11 ] [ 12 ] As of 15 June 2022, GenBank release 250.0 has over 239 million loci , 1,39 trillion nucleotide bases, from 239 million reported sequences.