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BioCodeKb - Bioinformatics Knowledgebase

Ensembl is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation and provides a single point of access to annotated genomes for mainly vertebrate species. Ensembl annotate genes, computes multiple alignments, predicts regulatory function and collects disease data. Ensembl is a bioinformatics project to organize biological information around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of individual genomes and of the synteny and orthology relationships between them. It describes a gene or genomic region in detail.

The Ensembl genome annotation system was developed jointly by the EBI and the Wellcome Trust Sanger Institute for the annotation, analysis and display of vertebrate genomes since 2000.

The goal of Ensembl is therefore to automatically annotate the genome, integrate this annotation with other available biological data and make all this publicly available via the web. Many more genomes have been added to Ensembl and the range of available data has also expanded.

The number of people involved in the project has also steadily increased. Currently, the Ensembl group consists of between 40 and 50 people, divided in a number of teams.

Ensembl Genomes is developed by EMBL-EBI and is powered by Ensembl software system for the analysis and visualization of genomic data. The genome list is as followed;

Ensembl Bacteria

Release 47 of EnsemblBacteria has updated pan-taxonomic gene trees and homologies.

Ensembl Fungi

Release 47 of Ensembl Fungi has updated protein features, BioMarts and pan-taxonomic compara data.

Ensembl Metazoa

Release 47 of Ensembl Metazoa adds Anopheles Christyi genome from VectorBase

Ensembl Plants

Release 47 of Ensembl Plants adds pineapple (Ananas comosus), Chara braunii, Eragrostis curvula, golden apple (Malus domestica), wild olive tree (Olea europaea sylvestris), pistachio (Pistacia vera), almond (Prunus dulcis) and supports Theobroma cacao cultivars Matina and Criollo.

Ensembl Protists

Release 47 of Ensembl Protists contains updated protein features, BioMarts and pan-taxonomic compara data.

Ensembl genes are based on mainly cDNA and protein evidence in scientific databases. The Ensembl annotation pipeline is combined with Havana manual annotation for the major species (human, mouse, zebrafish, pig and rat). Comparative analyses, sequence variation and regulatory features are all included in Ensembl.

Ensembl provides a number of ready-made tools for processing both our data and yours;

  • BioMart


  • File Chameleon

  • Data Slicer

  • Assembly Converter

  • Linkage Disequilibrium Calculator

  • Variant Effect Predictor (VEP)

We can use Ensembl when;

  • have a gene of interest, and we would like to know if there are homologues in other species, or any sequence variations in the gene

  • would like to know what the sequence is for our gene of interest

  • want to explore the region around a gene of interest, and find neighbouring genes

  • want to find sequences that may be involved in gene regulation are interested in how conserved a gene or region is across species;

  • want to know a selection of sequence variants that have been associated with a disease, for example, diabetes;

  • have questions about a gene, variant, or chromosomal region;


Need to learn more about ENSEMBL and much more?

To learn Bioinformatics, analysis, tools, biological databases, Computational Biology, Bioinformatics Programming in Python & R through interactive video courses and tutorials, Join BioCode.

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