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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.
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.
[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).
Eukaryotic gene-finding system: Eukaryotes [31] GrailEXP Predicts exons, genes, promoters, polyas, CpG islands, EST similarities, and repeat elements in DNA sequence: Human, Mus musculus, Arabidopsis thaliana, Drosophila melanogaster [32] [33] mGene Support-vector machine (SVM) based system to find genes: Eukaryotes [34] mGene.ngs
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 sequence identifiers table presents transcript information in VEGA, Ensembl and Blink. The chromosome location table includes the genomic coordinates for each ...
In 2013 Roche announced that they would be shutting down development of 454 technology and phasing out 454 machines completely in 2016 when its technology became noncompetitive. [ 15 ] [ 16 ] Roche produces a number of software tools which are optimised for the analysis of 454 sequencing data. [ 17 ]
In 2010, BGI bought 128 Illumina HiSeq 2000 gene-sequencing machines, [3] [17] which was backed by US$1.5 billion in "collaborative funds" over the next 10 years from the state lender China Development Bank. [5] [23] [24] By the end of the year, they reportedly had a budget of $30 million. [25]
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.