A utility like UCSC liftover

Oct 6, 2011 at 12:42 PM

Just wondering if MBF supply a liftover utility like the one provided by UCSC http://genome.ucsc.edu/cgi-bin/hgLiftOver 

Oct 7, 2011 at 11:01 PM

The LiftOver utility provided by UCSC converts genome annotations from one assembly to another. This requires a defined transform between the source and target assembly, or a route from source to target via intermediate assemblies – for the UCSC utility, these transforms are supplied in the form of chain files.

MBF does not provide equivalent functionality currently; while some of the groundwork to support annotations has been done, MBF as a whole does not yet contain a full-featured annotation model. This is one of the things we would like to see added to MBF by the community, and would appreciate any feedback on what the requirements would be, how it would be used by the community, and how to improve on the current LiftOver utility. We would be happy to provide assistance to any programmer interested in extending MBF in this way.

An alternative would simply be to port LiftOver to .NET – if done correctly, the resulting application could run on Windows, Linux and other platforms.

Rick Benge for the MBF team