Difference between revisions of "Ensembl"
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The Ensembl database provides annotation of genes from the [http://www.ensembl.org/index.html Ensembl genome databases]. | The Ensembl database provides annotation of genes from the [http://www.ensembl.org/index.html Ensembl genome databases]. | ||
| − | + | Ensembl database is available for different species. Usually [[BioUML]] installation contains Ensembl for human, mouse and rat, though it's possible to install other species as well. The installed Ensembl databases appear under the '''Databases''' tab. | |
| − | The | + | The following collections are available in BioUML Ensembl database: |
| + | * '''Data''': informational data elements. Information about them is available in [[information box]]. These collections can be searched using [[Lucene search]]. | ||
| + | ** '''gene''': list of all genes with annotation; | ||
| + | ** '''variation''': list of all variations with annotation (available if variation database is installed) | ||
| + | * '''Sequences''': list of chromosomes represented as {{Type link|sequence|sequence elements}}. They can be opened in [[genome browser]]. | ||
| + | * '''Tracks''': list of {{Type link|track}}s, which can be added to [[genome browser]]: | ||
| + | ** '''Karyotype''': karyotype (chromosome bands) display; | ||
| + | ** '''GC content''': graph displaying the local density of GC nucleotides; | ||
| + | ** '''Genes''': genes with exon-intron structure (including non-coding, pseudogenes, etc.); | ||
| + | ** '''ExtendedGeneTrack''': an alternative gene track where all genes are displayed in single line; | ||
| + | ** '''Repeats''': repeats regions (like Alu); | ||
| + | ** '''Variations''': SNPs and other known genomic variations (available if variation database is installed). | ||
==See also== | ==See also== | ||
*[[Databases]] | *[[Databases]] | ||
| − | *[[ | + | *[[Lucene search]] |
*[[Genome browser]] | *[[Genome browser]] | ||
*[[Ensembl installation]] | *[[Ensembl installation]] | ||
Revision as of 15:14, 26 June 2013
| This page or section is a stub. Please add more information here! |
The Ensembl database provides annotation of genes from the Ensembl genome databases. Ensembl database is available for different species. Usually BioUML installation contains Ensembl for human, mouse and rat, though it's possible to install other species as well. The installed Ensembl databases appear under the Databases tab.
The following collections are available in BioUML Ensembl database:
- Data: informational data elements. Information about them is available in information box. These collections can be searched using Lucene search.
- gene: list of all genes with annotation;
- variation: list of all variations with annotation (available if variation database is installed)
- Sequences: list of chromosomes represented as
sequence elements. They can be opened in genome browser.
- Tracks: list of
tracks, which can be added to genome browser:
- Karyotype: karyotype (chromosome bands) display;
- GC content: graph displaying the local density of GC nucleotides;
- Genes: genes with exon-intron structure (including non-coding, pseudogenes, etc.);
- ExtendedGeneTrack: an alternative gene track where all genes are displayed in single line;
- Repeats: repeats regions (like Alu);
- Variations: SNPs and other known genomic variations (available if variation database is installed).
