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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.
The web server or database management system also varies. LEMP is a version where Apache has been replaced with the more lightweight web server Nginx. [6] A version where MySQL has been replaced by PostgreSQL is called LAPP, or sometimes by keeping the original acronym, LAMP (Linux / Apache / Middleware (Perl, PHP, Python, Ruby) / PostgreSQL). [7]
The Ensembl website provides extensive information on how to install and use the API. This software can be used to access the public MySQL database, avoiding the need to download enormous datasets. The users could even choose to retrieve data from the MySQL with direct SQL queries, but this requires an extensive knowledge of the current ...
The EMBL Nucleotide Sequence Database (EMBL-Bank) has increased in size from around 600 entries in 1982 to over 2.5×10 8 by December 2012. [16] The EMBL Nucleotide Sequence Database (also known as EMBL-Bank) is the section of the ENA which contains high-level genome assembly details, as well as assembled sequences and their functional annotation.
pip (also known by Python 3's alias pip3) is a package-management system written in Python and is used to install and manage software packages. [4] The Python Software Foundation recommends using pip for installing Python applications and its dependencies during deployment. [5]
The Browser is a graphical viewer optimized to support fast interactive performance and is an open-source, web-based tool suite built on top of a MySQL database for rapid visualization, examination, and querying of the data at many levels. The Genome Browser Database, browsing tools, downloadable data files, and documentation can all be found ...
Ensembl encompasses a publicly available genome database which can be accessed via a web browser. The stored data can be interacted with using a graphical UI, which supports the display of data in multiple resolution levels from karyotype, through individual genes, to nucleotide sequence.
DECIPHER is a web-based resource and database of genomic variation data from analysis of patient DNA. [ 1 ] [ 2 ] [ 3 ] It documents submicroscopic chromosome abnormalities ( microdeletions and duplications ) and pathogenic sequence variants (single nucleotide variants - SNVs, Insertions, Deletions, InDels), from over 25000 patients and maps ...