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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.
Almost half of this data was deposited in relation to the 1000 Genomes Project [23] wherein the researchers published their sequence data to the SRA in real-time. [26] In total, as of September 2010, 65% of the Sequence Read Archive was human genomic sequence, with another 16% relating to human metagenome sequence reads.
1000 Genomes Project: launched in January 2008. The genomes of more than a thousand anonymous participants from a number of different ethnic groups were analyzed and made publicly available. EggNOG Database: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. It provides ...
Four novel alternative genetic codes were discovered in bacterial genomes by Shulgina and Eddy using their codon assignment software Codetta, and validated by analysis of tRNA anticodons and identity elements; [3] these codes are not currently adopted at NCBI, but are numbered here 34-37, and specified in the table below.
Originally centered on vertebrate animals as its main field of interest, since 2009 Ensembl provides annotated data regarding the genomes of plants, fungi, invertebrates, bacteria and other species, in the sister project Ensembl Genomes. As of 2020, the various Ensembl project databases together house over 50,000 reference genomes. [13]
Reference annotations of genomes are available from various sources, each with their own independent goals and policies, which results in some annotation variation. The CCDS project was established to identify a gold standard set of protein-coding gene annotations that are identically annotated on the human and mouse reference genome assemblies ...
The following versions of GFF exist: General Feature Format Version 2, generally deprecated . Gene Transfer Format 2.2, a derivative used by Ensembl; Generic Feature Format Version 3