How to visualise syntenic regions


We don't have a separate display for visualising these regions as chromosome blocks as for the moment, only one species (Anopheles gambiae) has it's whole genome assigned to chromosomes.

VectorBase has precomputed tBLAT (translated BLAT) DNA-DNA comparisons for Anopheles gambiae, Aedes aegypti and Culex quinquefasciatus. In the VectoBase genome browser, select the gene, genes or region you are interested in (Location tab). In the left hand menu, select "Comparative genomics -> Alignment (image)". Using the drop down menu in the middle of the page, select the species against which you would like to see the alignment. The link "Go to a graphical view" is below this drop down menu. After this option is activated it is also possible to select "Multi-species view" from the left hand menu. Use the "Configure this page" button on the left and later "Select Species" to add or remove a species.

It is also possible to access this data programmatically by querying against the Compara database at VectorBase (database available upon request), but it would take quite a lot of time to learn how to do this unless you are already familiar with the Ensembl Compara perl API.