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Old 10-29-2014, 08:38 AM   #1
James88
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Location: Leicester

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Default 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!
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Old 10-30-2014, 12:34 AM   #2
WhatsOEver
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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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Old 10-30-2014, 09:58 AM   #3
JohnN
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prokka uses Prodigal (http://prodigal.ornl.gov/) for its ORF predictions.
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Old 11-05-2014, 02:41 AM   #4
James88
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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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Old 11-05-2014, 03:22 PM   #5
fahmida
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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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Old 11-06-2014, 11:13 AM   #6
James88
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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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