Ensembl Database
From LMU BioDB 2013
- The database accessed is called Ensembl http://uswest.ensembl.org/index.html
- The purpose of this database is to collect, organize and distribute data resources to help support research regarding the genetics and genomics of chordates. [1]
- Ensembl contains genome information for 70 species. There is a focus on humans and major vertebrate model organisms, for example, the mouse, zebrafish and rat. [2]
- Ensembl contains 70 species on their site. Of these 70, and 58 have full gene annotations. For a list of all the species contained on Ensembl, follow this link : http://uswest.ensembl.org/info/about/species.html
- Ensembl is used for a variety of purposes. Data is imported from a variety of sources to create variation resources for 17 of their species, which can tell them about all the mutations in a genome. It also provides a great deal of regulation information on genes and are able to use comparative genomics when looking at the phylogenetic trees made by their species. [3]
- This database is focused on the structure model organism and mapping out the genes on each chromosome. It is curated electronically, and uses meta analysis in conjunction with UCSC and NCBI [4].
- Ensembl is maintained jointly between the European Bioinformatics Institute (EBI), which is a subsection of the European Molecular Biology Lab (EMBL) and the Wellcome Trust Sanger Institute (WTSI). Both the EBI and the WTSI are located on the same campus in Hinxton, United Kingdom.
- A majority of the funding for Ensembl comes from the Wellcome Trust, although they also receive funding from the National Human Genome Research Institute, the EMBL, and the Biotechnology and Biological Science Research Council. [5]
- All information can be publicly accessed on Ensembl. Ensembl has a license agreement stating that data can be redistributed, but it must be properly copyrighted back to them.
- Ensembl is updated on a monthly basis, and was last updated at the beginning of September.
- When Ensembl imports data from other sources, it links back to the original resource of information. [6]
- Information can be downloaded in a variety of ways, and can run up to many gigabytes of information. Data can be downloaded in the following file formats: FASTA, annotated sequence, MySQL, GTF, EMF flatfile dumps, GVF, BED format files, Tarball
- The website is very user friendly and very organized. At the top, the first button on the navigation bar is called “Using This Website” clicking on it brings you to a help page with a navigation bar on the side leading to brief tutorials of the site’s features.
- For the sample query we looked up genes associated with the phenotype coronary heart disease. The results made sense. It first led us to a page with links to specific genes and then allowed us to view the section of a chromosome on which the gene is located. Then it allowed you to click on a specific gene and told you its location and some detailed information about SNPs.
- This answer made sense and was very informative and detailed.
