Hi Eleni,
Although progressiveMauve's algorithm is deterministic for a fixed
input, the algorithm itself contains some stochastic elements,
especially when aligning regions between the initial set of unique
alignment anchors. Therefore, changes to the input such as order of
genomes, or possibly ordering of contigs within genomes, can change the
resulting alignment.
It sounds like your one of your genomes contains a potential
rearrangement, possibly related to repeat elements, that has a score
very close to the default LCB score thresholds being used by
progressiveMauve. Although the default parameters were tuned to produce
good results on a wide range of datasets there is nothing sacred about
them, they can be changed to produce better results if necessary. I do
wonder if a positional homology alignment might miss part of the
picture on your data though, it may be worthwhile to check for repeat
structure across your genomes using another method.
Best,
-Aaron
On Wed, 2017-03-01 at 12:09 -0600, Eleni Mijalis wrote:
> Images didn't come through, sorry. Please see attached.
>
> On Wed, Mar 1, 2017 at 12:01 PM, Eleni Mijalis <elenimija...@tamu.edu
> > wrote:
> > Hey there,
> >
> > I am having issues with getting different alignment results based
> > on the ordering of input files.
> >
> > I am aligning 7 genomes, and this is these are two examples of
> > alignments differing based on order:
> >
> >
> >
> >
> > As you can see, the first example gives 1 LCB spanning the entirety
> > of all the genomes, and the second example (same genomes, different
> > order) has more LCBs spanning different areas of each genome. These
> > two are just samples of what output I get based on input
> > permutation.
> >
> > I am using default parameters, so should I adjust parameters to get
> > more consistent results? Why would ordering matter when determining
> > regions of similarity? Thanks for your help.
> >
> > Eleni
> >
> -------------------------------------------------------------------
> -----------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> _______________________________________________
> 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.
------------------------------------------------------------------------------
Announcing the Oxford Dictionaries API! The API offers world-renowned
dictionary content that is easy and intuitive to access. Sign up for an
account today to start using our lexical data to power your apps and
projects. Get started today and enter our developer competition.
http://sdm.link/oxford
_______________________________________________
Mauve-users mailing list
Mauve-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/mauve-users
