Hello. I just wanted to follow up on my email below. Thoughts from anyone? Thanks for your help in advance!
Taruna > On Nov 26, 2015, at 7:47 AM, Taruna Aggarwal <ta2...@wildcats.unh.edu> wrote: > > I have a de novo assembly of a fungus and I’m trying to generate synteny > maps for it. I would like to use pMauve aligner to accomplish this goal but I > have some questions regarding the program and the results I’ve been getting. > > Initially I ran pMauve aligner with all default parameters to get a sense of > the program. Next, I changed a few parameters and got the alignment results > that do not show large syntenic blocks for a self to self alignment > (Grosmannia_clavigera_genome to Grosmanni_clavigera_genome). Additionally, I > expected more syntenic regions between my two genomes of interest > (gm5_allpaths_scaffolds aligned to Grosmannia_clavigera) than the results > show. I have been changing the LCB weight around and when I choose a small > value, there are several LCB connecting lines. I understand what LCBs are but > I don’t understand what changing the LCB weight does to the alignment. > Lastly, if anyone has any suggestions as to which parameters I should change, > I would really appreciate them. Thank you very much for your help! I have > attached screenshots of the alignments in question and the parameters I used. > Please let me know if I can clarify anything. Thanks again! > > Taruna > > <Screen Shot 2015-11-25 at 10.40.54 AM.png> > <Screen Shot 2015-11-25 at 4.46.01 PM.png><Screen Shot 2015-11-25 at 4.45.45 > PM.png> > ------------------------------------------------------------------------------ Go from Idea to Many App Stores Faster with Intel(R) XDK Give your users amazing mobile app experiences with Intel(R) XDK. Use one codebase in this all-in-one HTML5 development environment. Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140 _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
