Thread: Re: [Mauve-users] genome ordering
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koadman
From: Eleni M. <ele...@ta...> - 2017-03-01 18:17:36
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Images didn't come through, sorry. Please see attached. On Wed, Mar 1, 2017 at 12:01 PM, Eleni Mijalis <ele...@ta...> 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: > [image: Inline image 1] > > [image: Inline image 2] > > 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 > |
From: Aaron D. <aar...@ut...> - 2017-03-08 22:22:07
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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 <ele...@ta... > > 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 > Mau...@li... > 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. |