Body: <p>I apologise for very basic question but I am very new to biology and have very specific knowledge of this field, I am currently working on Bioinformatics in my machine learning project which is why I need to be sure about obtained results before I proceed. I am not aware of all the tools used in genomics/bioinformatics. I would like to know that what tools can be used if I want to trace and observe the strand orientations in the ancestral inversion mutations? I would like to know the key concepts as well, using which I can automate the process in my program and display the orientation.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-07-29T14:34:05.270Z
Comments.Text: Hi @Pragati I dunno its difficult to understand your project. Could you define your question, e.g. organism, distrubution. What are is your training sett ... input and output?
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-07-29T19:20:45.130Z
Comments.Text: The question you are asking can be done via phylogeny, HOWEVER your project is to use ML, DNN instead of phylogeny. Personally, I wouldn't fancy taking on the question, because in my view there is too much we don't know. It is just my opinion however.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-07-30T10:14:18.613Z
Comments.Text: Completely agree that this sounds like a phylogeny project. For a software to find genomic rearrangements (inversions and the like), you can check out Mauve: http://darlinglab.org/mauve/user-guide/introduction.html . But you'll need to break up your project into questions that you can actually tackle, and acquire a lot of domain knowledge.
Comments.UserDisplayName: csgroen
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-07-30T10:24:21.963Z
Comments.Text: @Michael I need to analyse the inversion mutations: Any tool to do this directly will be useful. Thanks for your suggestion I will look into details.
Comments.UserDisplayName: Pragati Bhingare
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-07-30T10:28:01.937Z
Comments.Text: @csgroen I agree that I will have to acquire more knowledge if I am tackling tricky bits of the project. I'll check out the software. Thank you
Comments.UserDisplayName: Pragati Bhingare
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-07-30T10:41:46.400Z
Comments.Text: "inversion mutations" I dunno, I do genetic mechanisms but I don't really understand the term. Is this a reference to a locus, or some sort of compensatory mutation? If it is a inverted locus, is it a reference to the "inversion" as being the mutation?
Comments.UserDisplayName: M__
Tags: <phylogenetics><genomics>
Title: "How the clustal omega can be reverse engineered, to trace ancestral inversion mutations via the guide tree?"
ThreadText: # "How the clustal omega can be reverse engineered, to trace ancestral inversion mutations via the guide tree?"
  
  (Asked by: username_0 on 2020-07-29)
  
  I apologise for very basic question but I am very new to biology and have very specific knowledge of this field, I am currently working on Bioinformatics in my machine learning project which is why I need to be sure about obtained results before I proceed. I am not aware of all the tools used in genomics/bioinformatics. I would like to know that what tools can be used if I want to trace and observe the strand orientations in the ancestral inversion mutations? I would like to know the key concepts as well, using which I can automate the process in my program and display the orientation.
  
  **Tags:** phylogenetics, genomics
  
  > **Comments:**
  > **username_1**: Hi @username_0 I dunno its difficult to understand your project. Could you define your question, e.g. organism, distrubution. What are is your training sett ... input and output?  
  > **username_1**: The question you are asking can be done via phylogeny, HOWEVER your project is to use ML, DNN instead of phylogeny. Personally, I wouldn't fancy taking on the question, because in my view there is too much we don't know. It is just my opinion however.  
  > **username_2**: Completely agree that this sounds like a phylogeny project. For a software to find genomic rearrangements (inversions and the like), you can check out Mauve: http://darlinglab.org/mauve/user-guide/introduction.html . But you'll need to break up your project into questions that you can actually tackle, and acquire a lot of domain knowledge.  
  > **username_0**: @Michael I need to analyse the inversion mutations: Any tool to do this directly will be useful. Thanks for your suggestion I will look into details.  
  > **username_0**: @username_2 I agree that I will have to acquire more knowledge if I am tackling tricky bits of the project. I'll check out the software. Thank you  
  > **username_1**: "inversion mutations" I dunno, I do genetic mechanisms but I don't really understand the term. Is this a reference to a locus, or some sort of compensatory mutation? If it is a inverted locus, is it a reference to the "inversion" as being the mutation?  
  
  ---
  
  ## 0 answers
  
  