Hi, I want to identify polymorphic regions between different closely-related genomes and therefore use the XMFA file produced in the progressiveMauve alignment. I would like to exclude regions around contig borders (using a self-written script) to focus only on reliable polymorphic regions.
However, I cannot figure out how the contig borders are stored in the Mauve output files. There is no special symbol in the alignment and I do not find the coordinates of the contig borders in one of the other output files. Is there a way to derive the coordinates of the contig borders shown in the viewer by the red vertical lines directly from the outputfiles? Thanks, Thomas -- M.Sc. Thomas Weinmaier Department of Computational Systems Biology University of Vienna Althanstraße 14 A-1090 Vienna Phone: +43-1-4277-762 13 Email: [email protected] ------------------------------------------------------------------------------ Write once. Port to many. Get the SDK and tools to simplify cross-platform app development. Create new or port existing apps to sell to consumers worldwide. Explore the Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join http://p.sf.net/sfu/intel-appdev _______________________________________________ Mauve-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mauve-users
