Ensembl genome database project

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Ensembl Genome Database Project is a comprehensive and integrated computational resource for accessing and analyzing genome data for a wide variety of species. The project aims to provide a centralized platform for geneticists, researchers, and scientists to explore and understand the genetics and genomics of organisms ranging from humans to model organisms and other species of scientific interest.

Overview

The Ensembl project was initiated in 1999 as a joint effort between the European Molecular Biology Laboratory (EMBL) and the Wellcome Trust Sanger Institute to develop a software system capable of automatically annotating genomes, integrating this information with other available biological data, and making all these data freely available via the web. The project supports data from both vertebrate and invertebrate species, providing tools for gene annotation, genome browsing, and comparative genomics.

Features

Ensembl offers a variety of features to its users, including:

• Gene Annotation: Automated annotation of gene sequences, including the identification of coding sequences and the prediction of gene structure.
• Genome Browser: An interactive web interface for viewing the genome sequence of numerous species, along with annotations and comparative genomics data.
• Comparative Genomics: Tools and data for comparing the genetic content and organization across different species, aiding in the study of evolution and functional genomics.
• Variant Effect Predictor: A tool for predicting the functional effects of known and unknown variants on genes, transcripts, and protein sequence, as well as regulatory regions.

Data Access

Ensembl provides several ways for users to access its data:

• Web Interface: A user-friendly web interface for browsing and searching the database.
• Application Programming Interface (API): A set of programming interfaces for fetching Ensembl data programmatically, available in Perl and REST.
• BioMart: A data mining tool for complex queries across multiple datasets and species.
• FTP Site: Bulk data downloads in various formats are available through the Ensembl FTP site.

Supported Species

Ensembl's database includes a wide range of species, from well-studied model organisms like the mouse, fruit fly, and zebrafish, to agricultural animals like the cow and pig, and of course, humans. The project continually adds new genomes based on scientific interest and community demand.

Collaborations and Extensions

Ensembl collaborates with several other bioinformatics projects and databases to enhance its offerings, including:

• 1000 Genomes Project: Integrating human variation data from the 1000 Genomes Project.
• GENCODE: Providing comprehensive annotation of gene features in the human genome.
• TreeFam: Offering phylogenetic tree data to support comparative genomics analysis.

Future Directions

The Ensembl project is committed to expanding its database with new species, improving the accuracy of its annotations, and developing new tools for genome analysis. The project aims to adapt to the rapidly evolving field of genomics by incorporating new data types and technologies, such as long-read sequencing and single-cell genomics.

See Also

• Genomics
• Bioinformatics
• Genome Project
• Comparative Genomics