The default parameters appear to work reasonably well over a range of divergences although at higher levels of nucleotide divergence, e.g. <65% identity, the aligner begins to lose sensitivity. When this happens some positionally homologous sites fail to become aligned. This issue is characterized in the x-axis series of figure 5 in the progressiveMauve manuscript (Darling et al 2010 PLoS ONE): http://www.plosone.org/article/info%3Adoi%2F10.1371% 2Fjournal.pone.0011147
where you can also see how it affects some other aligners. On Wed, 2014-11-12 at 16:54 +0100, Anja Friedrich wrote: > Dear Aaron, > > I did not imply a bug, maybe there is something with the settings I used to > create the SuperGenome. I was just wondering if the default settings for the > progressiveMauve algorithm were acceptable if I have varying degrees of > similarity between the genomes? > > Kind regards, > Anja > > -----Original Message----- > From: Aaron Darling [mailto:aaron.darl...@uts.edu.au] > Sent: Tuesday, 11 November 2014 11:33 p.m. > To: mauve-users@lists.sourceforge.net > Subject: Re: [Mauve-users] alignment of 15 genomes with varying degrees of > similarity > > Hello Anja, > > On Tue, 2014-11-11 at 14:32 +0100, Anja Friedrich wrote: > > > I am trying to align 15 genomes of Campylobacter jejuni that belong to > > different sequence types and therefore vary in their similarity to > > each other. I would like to use the resulting xmfa to create a > > SuperGenome of all 15 genomes. However, the coordinate space of some > > genomes doesn’t seem to make sense (e.g. space is longer than the > > genome, or negative coordinates). Which parameters would I have to > > change to get a more sensible alignment of the 15 genomes? Any help > > would be appreciated. > > > The coordinate system represents a concatenation of all contigs/scaffolds in > the assembly. If the genomes have plasmids then these will add to the length. > The negative numbers represent regions that are in the reverse-complement > orientation relative to the other genomes that contain the region. Given the > amount of testing & use the aligner has had over the years I would be quite > surprised to learn of a bug that is causing progressiveMauve to produce > coordinates that extend beyond the available genomic sequence, however it's > certainly not impossible. If it's still not right after taking the above > suggestions into account I'd like to do a thorough investigation with your > dataset. > > 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. > ------------------------------------------------------------------------------ > Comprehensive Server Monitoring with Site24x7. > Monitor 10 servers for $9/Month. > Get alerted through email, SMS, voice calls or mobile push notifications. > Take corrective actions from your mobile device. > http://pubads.g.doubleclick.net/gampad/clk?id=154624111&iu=/4140/ostg.clktrk > _______________________________________________ > Mauve-users mailing list > Mauve-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/mauve-users > > ------------------------------------------------------------------------------ > Comprehensive Server Monitoring with Site24x7. > Monitor 10 servers for $9/Month. > Get alerted through email, SMS, voice calls or mobile push notifications. > Take corrective actions from your mobile device. > http://pubads.g.doubleclick.net/gampad/clk?id=154624111&iu=/4140/ostg.clktrk > _______________________________________________ > Mauve-users mailing list > Mauve-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/mauve-users -- 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. ------------------------------------------------------------------------------ Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://pubads.g.doubleclick.net/gampad/clk?id=154624111&iu=/4140/ostg.clktrk _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
