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.

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    $\begingroup$ 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? $\endgroup$
    – M__
    Jul 29, 2020 at 14:34
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    $\begingroup$ 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. $\endgroup$
    – M__
    Jul 29, 2020 at 19:20
  • $\begingroup$ 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: 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. $\endgroup$
    – csgroen
    Jul 30, 2020 at 10:14
  • $\begingroup$ @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. $\endgroup$ Jul 30, 2020 at 10:24
  • $\begingroup$ @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 $\endgroup$ Jul 30, 2020 at 10:28


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