Ensembl HelpView

The Ensembl project provides automated genome annotation and subsequent visualisation of the annotated genomes. The generic URL for the project page is http://www.ensembl.org/. The main page gives introductory information and links to species-specific data sets, as well as additional documentation.

Each species supported by Ensembl has its own home page. Species-specific home pages normally provide:

• Key entry points for access to the data.

• Basic release information and statistics.

• A link to a clickable site map for further information and additional entry points into the Ensembl system.

The Ensembl Pre! release site displays preliminary data sets for genomes currently in the process of analysis and annotation. These preliminary sets may represent genome sequence assemblies for new species, or new assemblies for existing species. It is provided as an "early access" site for our users and shown after the initial BLAST analysis has been completed. As the gene-build has not been completed at this stage, Ensembl gene sets and additional informations are not available. Consequently, not all Ensembl displays will be available. The fully annotated genome will be released after the gene-build has been completed and as soon as we are confident with the quality of annotation. Tentative release dates are always available from the preliminary Ensembl site.

About Ensembl

See the 'generic' Ensembl home page for basic information and links to documentation, including an introductory 'tour', detailed worked examples for you to try, and links to published papers about Ensembl.

Throughout the web site, clicking on the button will pop up a window containing context-sensitive help. You may also search the help database using the box provided at the top of this window. Click on to see a list of all available "Help" and "How Do I..." pages.

Ensembl Entry Points

You can carry out a search across all the species within Ensembl at the top of the generic Ensembl home page. For species-specific searches, use the species pages.

You can enter the multi-species EnsMart data mining system via each species or from the generic home page.

The species home pages provide several ways to access the data in Ensembl.

Search

This allows you to search the whole Ensembl database of genomic information, or categories of information within it. On the generic Ensembl home page you can carry out a search across all the species within Ensembl. On a species homepage (or from any other page within the web site), searches are limited to a single species.
More help on Ensembl Search

Display Chromosome

Enter a chromosome number and a location on that chromosome (in base pairs by default, or specify kb or Mb) to jump to a 'ContigView' display of the features in that region.

Retrieve a sequence

Jump to 'ExportView' pages to download a region of the genomic sequence, with or without annotation.

Advanced data retrieval tool

Jump to 'EnsMart' to mine the database for genes of interest and for SNPs. Annotated lists and sequence sets are available.

BLAST

To locate regions in the genome (or predicted transcripts and proteins) that have sequence similarity to your own sequence of interest.

SSAHA or BLAT

Try SSAHA or BLAT, fast algorithms for similarity searching.

Browse a Chromosome

Clicking on any chromosome will take you to the corresponding 'MapView' page, which will allow you to select a region to view by clicking on a band, specify a chromosome region using marker names, jump to a view of regions in other species where synteny is conserved (available between human, mouse and rat) and to see basic statistics on that chromosome.

Documentation and help

Links to documentation and help resources.

Ensembl links and site map

Quick links, plus click on the map for an easy-to-use clickable map of Ensembl resources.

Other Species

"Other Species" provides links to other organisms' genomes annotated by Ensembl.