New in this release (version 65 of Ensembl) is the ability to save your selected tracks as a configuration.  You can load in a set of tracks you chose with a simple click of the ‘Load configuration’ button.  A simple example follows.

From the Region in detail view, click on Configure this page.  Choose some tracks, for example, in the dbSNP menu: ‘Sequence variants (dbSNP and all other sources)’, in the EST alignments menu: ‘Human EST’, and in the RNA-Seq models menu: ‘blood intron’ and ‘blood’.  Now click the Save as button at the bottom left of the menu.

Name the configuration as My Tracks 1.  You can add a description as well, for example I selected SNPs, ESTs, and RNA-Seq blood models.  Click Save.

Now you have a configuration named My Tracks 1!  Even if you deselect the tracks and turn other data on, you can always go back to this selection by clicking on Configure this page and then Load configuration.

Try it on other views like Gene summary!

Clicking on Configure this page allows acess to the Manage configurations tab.  Here, you can make a configuration set.  A configuration set allows tracks across many different Ensembl views to be switched on all at once.

We hope you find this useful!  Keep your eyes out for future sharing of configuration, making it easy to send ‘your Ensembl view’ to a lab mate or colleague.

 

 

 

The Ensembl Genomes Project is pleased to announce release 11 of Ensembl Genomes.

This release contains 7 new genomes.  Main highlights are:

* Software migration to Ensembl 64

* Cross-references to PHI-base, a database of pathogen-host interactions, added to genomes in Ensembl Protists

* Mycosphaerella graminicola and Phaeosphaeria nodorum (major wheat pathogens), along with Tuber melanosporum (symbiotic Perigord Truffle) included in Ensembl Fungi

* Three new genomes in Ensembl Plants: Glycine max (soybean), the spikemoss Selaginella moellendorffii and the green algae Chlamydomonas reinhardti, along with updates to the Oryza glaberimma (African rice) genome and to the gene models of Vitis vinifera (grape)

* Amphimedon queenslandica (demosponge) included in Ensembl Metazoa, along with updated gene models for Drosophila melanogaster and Drosophila pseudoobscura.

An urgent firmware update by sanger systems will result in downtime on the main site (www.ensembl.org) for 30 minutes (expected) at 4 PM UK time (BST) today, 9 September.  The services affected will be the websites (www.ensembl.org, archive sites, vega.sanger.ac.uk, pre.ensembl.org) and the MySQL servers (ensembldb.ensembl.org and martdb.ensembl.org).

Please use our mirror sites for web browsing and database queries.  The mirrors will be fully functional, apart from BLAST and user logins, and can be found here:

useast.ensembl.org, uswest.ensembl.org, or asia.ensembl.org

Thank you for your patience,

Ensembl Team

 

The team is looking forward to supporting our users in Japan!  For the next two weeks, one of our Ensembl outreach officers, Jana, will be teaching full day workshops at the DBCLS and Showa Pharmaceutical University in Tokyo, RIKEN in Yokohama, Osaka University in Osaka, and the OIST in Okinawa.  James from the EBI will also be introducing other EBI resources and tools such as Array Express, the Atlas, and Reactome.

More information can be found here.  We look forward to hearing from new and continuing Ensembl users in Japan!

We are looking for projects that use aspects of the Ensembl code (for example, the webcode, the genebuild pipeline, or comparative analyses).  If you want to be added to our list, please reply to this blog post, or email our helpdesk with your project name, url, and what aspect of the code you are using.

In addition to the projects on our powered by Ensembl page, we have heard from:

Let us know about your project!

 

We’d like to announce our beta site at beta.ensembl.org.  This site will allow us to show you the latest features of our website, and to get user feedback before new functionality and design are moved over to our live site.

Come by and try it out!  Leave us feedback by clicking on the black Feedback button at the right of beta pages.

Our latest features on the beta site are listed on the front page.  Two of the ones we’re most excited about are:

1) Track ordering on region in detail.  Want to change the order of data tracks on the genome?  Either use the bar at the left, or reorder them using Configure this page.  You can even move them all to one side of the chromosome (at the moment, Ensembl separates them by strand.)  See our help page for more.

2) Draw features for selected species in alignment views in the location tab.  For example, add a species to multi-species view.  Click on configure this page at the left.  A species menu is now shown, so you can draw data tracks for one species and not the other, if you like!  See the bottom of the help page for more about this functionality.

We have just updated the Ensembl genome browser and underlying databases to version 62.  We would like to share some new features with our user community.

The new Ensembl release hosts a new species- the white-cheeked gibbon (Nomascus leucogenys).  A new genebuild has been performed using the Ensembl gene annotation pipeline, incorporating both gibbon and human sequences to determine the gibbon gene set.   Compara has also incorporated the gibbon genes and genome into comparative genomics analyses, as is usual for new genebuilds.  Gibbon can now be found in gene trees, a pairwise whole genome alignment with human , and a 35-way multi-species alignment.  View these alignments in views like this one.

BigWig files are now supported through attachment of a url to Ensembl.  Click on ‘Manage your data’ at the left of a location page, and select ‘Attach Remote File’ from the new menu.

Not sure what Ensembl has to offer, or how to use our resources?  Now whenever you search for a term, hits to Help and Documentation will come up.  These may be to page-specific help, FAQs or the glossary, depending on the term.  As always, we hope our users make requests- if you can’t find what you’re looking for, let our helpdesk know.

Finally, SIFT and PolyPhen predictions are available in human variation pages, and in the popular Variant Effect Predictor (for human).  A more detailed post on these variation analyses will be coming soon, so keep your eye on the blog.

More features like the new comparative genomics navigation menu have been released, so explore and let us know what you think.  More news is available on our website.

The ENCODE project is generating an immense amount of data.  ChIP-Seq, ChIP-ChIP, and RNA-Seq experiments are yielding an exciting number of sequences that may be involved in gene regulation.  Trying to look at these data individually would be a lot of work, and less powerful, than viewing these data in combination.  The Ensembl Regulatory Build takes data such as CTCF binding sites, DNaseI hypersensitive sites, transcription factor binding sites, and histone modification profiles, and integrates these data into ‘regulatory features’.  The result is for any given regulatory feature in a specific region of the human genome, our users can learn 1) if there is data supporting that sequence as being involved in gene regulation (for example,  is it promoter associated) and  2) how much data supports the sequence as a regulatory feature.

For example, if we zoom in to BRCA2 in the Ensembl region in detail view, the regulatory feature at the 5’ end of the BRCA2-003 transcript is supported by data from numerous experiments (shown in the figure below).  Click on the grey block in the Reg. Feats. track in the region in detail view to see them.

 

 

 

 

 

You can even view regulatory features for a specific cell type.  Click on the Configure this page tool button at the left of the region in detail view to do so.  Or, try the regulation tab (get there by clicking on a regulatory feature’s stable ID, such as ENSR00000054736 in the image above).

Questions or comments about these data or views are welcome.  Reply to this post, or email our helpdesk by using the Contact us link at the top right of this blog.

Due to feedback on a recent survey, we decided to post some pointers to functionality that may not have been discovered by many of our users.  One specific case is viewing syntenic regions calculated by the Ensembl comparative genomics team (Compara).

How can we view these regions in the Ensembl genome browser?

There are two ways.  The first way is to go to the dedicated Synteny view.  This view, found in the location tab, offers a comparison of syntenic regions between two species.

In the above figure, a chromosome of interest (human chromosome 6)  is depicted in the centre, and any mouse chromosomes with synteny to human chromosome 6 are drawn as smaller chromosomes along the sides.  The colours of the syntenic blocks represent specific mouse chromosomes.

Compare with a different species, or change the central chromosome, using the menus beneath the figure.  A gene list comparing genes within the regions of synteny in both species can also be found below the image.  Read the page help for more.

The second way is to draw syntenic blocks along the chromosome in the Location tab, Region overview.  Click the Configure this page tool button at the left of the view to add synteny for one or multiple species.

If you have a topic you would like to see in a ‘navigation tip’ post, please leave us a comment, or email our helpdesk.

Ensembl 61 has gone live. In displays like gene summary and region in detail, favourite tracks can be turned on. To do this, open the configuration panel (click on configure this page in the left hand menu). Activating a star by clicking on it will place that track in the favourites menu (shown by an arrow in the diagram).

Hover over any track name in these views to view information about the data, change the display, or turn the track off. Turning on tracks must still be done with the configuration panel.

We hope this helps ease of navigation. Read about other updates in 61, such as our new species, Turkey, in the news. The Ensembl Team