Hi Sean, On Wed, 2010-10-20 at 07:47 -0400, Sean Li wrote: > Hi, Aaron, > > I have a few questions, and will appreciate your help very much. In the > old version of MAUVE (2.0.0), GRIMM Rearrangement History Analysis give > some extra data. However, where can I find the function in the new > version (2.3.0) analysis?
The GRIMM method only works when all genomes have equal gene content, or in this case equal LCB content. Since progressiveMauve can find regions conserved in subsets of the input genomes (unlike mauveAligner), the alignments created by progressiveMauve violate the assumptions made by GRIMM and related methods. Therefore the progressiveMauve alignment must be simplified before it can be analyzed with GRIMM or Double-Cut-Join (DCJ). One way to do that is to use the projectAndStrip or stripSubsetLCBs utilities, as outlined on this page: http://gel.ahabs.wisc.edu/~koadman/barphlye/ That will simplify the alignment to contain only "core genome" regions which are conserved among all genomes and thus suitable for analysis with GRIMM. Note that before reloading a simplified alignment back into the Mauve viewer, one must run it through the program "addUnalignedIntervals" to re-add the complete set of unaligned regions, since the Mauve viewer expects every base of each genome to exist in the XMFA file. One could then launch GRIMM and/or DCJ in the usual way. > When I start Mauve 2.3.0 in my standalone > computer, my machine told me "Could not create the Java Virtual > machine". Is my java corrupted? Possibly, I'm not familiar with this error message. Perhaps the Mauve java startup script is requesting more memory than that computer has? Do other java programs work? > After I have run for two weeks in an > analysis of 8 bacterial genomes using Mauve 2.0.0, an error listed below > occurred. Does that have some thing to do with the short of memory in > the machine? That's probably not a shortage of memory but more likely a bug in 2.0.0. All of the progressiveMauve releases between 2.0 and 2.3 had a few unfortunate bugs that would cause crashes. 2.3.1, which was released nearly a year ago, solves those issues. Hope that helps, -Aaron ------------------------------------------------------------------------------ Nokia and AT&T present the 2010 Calling All Innovators-North America contest Create new apps & games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
