Hi Shlomo, On Sun, 2013-09-15 at 20:39 +0200, Shlomo Blum wrote: > > 1. Should I reorder all the drafts against the same reference genome > from NCBI, or should I reorder the "control" strain first, and then > reorder the other strains against the reordered "control" strain > (after concatenating the contigs?)?
Without knowing what you mean by a "control" strain, or any of the details about how far diverged your control and other strains are from the NCBI reference, it's hard to say which approach would work better. In general progressiveMauve will run most efficiently if all draft genomes have been ordered against the same reference, where that reference is the closest possible match in terms of gene content and genome arrangement. > > 2. I am also using ACT to compare the genomes. Perhaps this question > should be sent to a different forum, but I wonder if I should create > comparison files of each genome against the "control" genome or to the > external reference genome from NCBI used during reordering? Yes, you might find more ACT expertise elsewhere. Best, -Aaron -- Aaron E. Darling, Ph.D. Associate Professor, ithree institute University of Technology Sydney Australia http://darlinglab.org twitter: @koadman UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. Think. Green. Do. Please consider the environment before printing this email. ------------------------------------------------------------------------------ LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151&iu=/4140/ostg.clktrk _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users