Navigation Tip- Viewing Synteny

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.