Help:How to visualise syntenic regions

From VectorBase Help System

You can use MultiContigView to help you visualise regions of conserved synteny. We don't have a separate display for visualising these regions as chromosome blocks, but we are thinking of introducing this in the future (within the mosquitoes).

VectorBase has precomputed tBLAT (translated BLAT) DNA-DNA comparisons for these 3 species. In ContigView you can turn on tracks showing these matches (use the 'Comparative' pull-down menu at the top of the detailed view panel).

You can jump to MultiContigView either from the pop-up obtained by pointing to one of those matches, or from the 'View alongside ...' option in the left side bar. In MultiContigView, related genes are shown joined, and you can also show and join the tBLAT matches. The region you mention is a bit of a mess when viewed against Anopheles because it has many closely related family members which give matches to one-another.

It is possible to access this data programmatically by querying against the 'compara' databases at Ensembl, 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. But please email again if you need to do this or have any other questions about using the web interface.

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