Hi Carmela, apologies for the delayed response. Without seeing the exact details of what you're observing, e.g. with a screenshot, it's hard for me to know whether this is actually a bug or some confusion in the interpretation of how the viewer displays the alignment. Just to clarify a bit: the XMFA is created by the progressiveMauve command-line software, and the Mauve GUI only provides a visual display of that XMFA format alignment. Gap characters are never displayed in the GUI: when zoomed all the way in to an alignment the individual nucleotides in the sequence will appear but an alignment gap is indicated only by the absence of the highlighting cursor in the gap genome when hovering the mouse over one of the other genomes which has sequence content in the gap region. SNPs will affect the similarity profile. A list of SNPs can be exported via the GUI, or extracted by parsing the XMFA.
Hope that helps, -Aaron On Tue, 2014-08-05 at 08:39 +1000, Carm C wrote: > Hi all, > > > I used progressiveMAUVE to align 4 bacterial genomes (~4Mb each), > which ran with no error. I need to now parse the text sequences to > pull specific positions from each (using the first sequence as a > reference for position number) for use as outgroups in a SNP tree. > However, I've noticed a seeming inconsistency in what I see in the > GUI representation of my alignment file versus what I see in the text > file. More specifically, the text file indicates that there should be > gaps (very long gaps in some cases) at certain positions in the first > sequence, but when I look at the corresponding position in the GUI > browser, I don't see any gaps at those positions in the first > sequence, and indeed see far fewer gaps in the GUI than what is > represented in the text file. As I need to pull thousands of specific > SNP positions, I'm not quite sure how to deal with this seeming > inconsistency. > > > Is there something fundamental I'm missing here? Hopefully this > question is clear. > > > Thanks in advance for any possible help! > Carmela C > SDSU Biological and Medical Informatics Research Center -- 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. ------------------------------------------------------------------------------ _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
