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  • Glimmer vs Prokka

    Hello,

    I am wondering if there is some cross-over in the functions of Glimmer and Prokka. As I understand it, Glimmer is able to predict orf's and extract them. Prokka is is used for annotation. Does Prokka therefore also do orf/gene prediction also?

    I've tried to see this for myself but am struggling to properly install Prokka. Glimmer seems to behave exactly as I'd expect.

    Thanks!

  • #2
    Yes, you are right.
    Glimmer is just for gene prediction, while prokka is a kind of all-in-one tools, doing both, gene prediction (or, to be more accurate "feature prediction" as not only genes but also rRNA and tRNA prediction can be included) and annotation.

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    • #3
      prokka uses Prodigal (http://prodigal.ornl.gov/) for its ORF predictions.

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      • #4
        Thank you for the help. It was all the encouragement I needed to carry on and get PROKKA working and ditch Glimmer!

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        • #5
          Good luck with Prokka installation. Though it is a handy tool, it has a scary list of requirements and I couldn't get over it in three attempts so far and gave up for now.

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          • #6
            I ended up giving up installing it on my Linux laptop and did a clean install of Linux on a partition of my Windows computer.

            Then installed on there and it worked... Didn't really SOLVE my problems but I can use it so I'll take that for now since it's the first step in my work.

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