I am trying to pull all the aligned sequences from the .xmfa generated by progressiveMauve using the coordinates in the .backbone file. Am I correct in believing that the coordinates in the defline of each .xmfa block should match those in the corresponding column of .backbone? If so, something is awry. I find cases of .backbone sequences present in all genomes that extend beyond the LCB in the .xmfa when I parse these coordinates. To make things worse, when I convert from ungapped (unaligned) coordinates (which I am assuming what the .backbone and .xmfa coordinates are) to gapped coordinates by counting the number of -'s and then take a slice of the alignment with bioperl, the sequences don't match up. I'm stumped.
I'd like to use stripSubsetLCBs but it gives the following error message on my Mac 10.5.8: Exception FileNotOpened thrown from Unknown() in gnFileSource.cpp 67 Called by Unknown() Read 24053 backbone entries seq_count is: 0 output_ivs.size() 24053 Segmentation fault Any pointers would be greatly appreciated. Thanks, Maren ------------------------------------------------------------------------------ Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
