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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.
[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).
Cervical cancer gene database; Ensembl: provides automatic annotation databases for human, mouse, other vertebrate and eukaryote genomes; Ensembl Genomes: provides genome-scale data for bacteria, protists, fungi, plants and invertebrate metazoa, through a unified set of interactive and programmatic interfaces (using the Ensembl software platform)
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.
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.
Also, the GENCODE website contains a Genome Browser for human and mouse where you can reach any genomic region by giving the chromosome number and start-end position (e.g. 22:30,700,000..30,900,000), as well as by ENS transcript id (with/without version), ENS gene id (with/without version) and gene name. The browser is powered by Biodalliance. [19]
The gene finder is based on a hidden Markov model (HMM) that is automatically estimated for a new genome. Prokaryotes [8] [9] EuGene: Integrative gene finding: Prokaryotes, Eukaryotes [10] [11] FGENESH: HMM-based gene structure prediction: multiple genes, both chains: Eukaryotes [12] FrameD: Find genes and frameshift in G+C rich prokaryote ...
Genes: Initial gene records are imported and updated from the National Center for Biotechnology Information's Gene database on a weekly basis. Data imported during this process includes the Gene ID, Genbank /RefSeq nucleotide and protein sequence identifiers, HomoloGene group IDs and Ensembl Gene, Transcript and Protein IDs.