Plugin documentation

Vsevolod Cherepashkin

• October 23, 2019 10:38

Hi all,

I just wanted to use plugin for drawing CpG islands.
https://www.geneious.com/plugins/cpg-islands-plugin/.

I don't understand exactly, what does it do, why there is black and green line, and green area, what does it mean. I didn't find any documentation or detailed plugin description.

Did someone meet the same problem?

Sincerely,
Vsevolod Cherepashkin
Leibniz Institute for Neurobiology Magdeburg, Germany
Neuroplasticity Department

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  Hilary Miller

  • October 23, 2019 22:35

  Here is some more information about this plugin:

  CpG Islands uses a well known Hidden Markov Model algorithm called the Forwards/Backwards algorithm to calculate the posterior probability of any residue being in a CpG Island, and uses state transition parameters from taken from p. 50 of R. Durbin, S. Eddy, A. Krogh, and G. Mitchison: Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, 1998.
  
  The green bars are the best global reconstruction - green indicates CpG island regions in the most likely global assignment of CpG islands to the sequence. 
  
  The black/green line is the per-site log odds ratio, green indicates that the site is probably part of a CpG island, taking all possible reconstructions into account. 

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  Vsevolod Cherepashkin

  • October 24, 2019 07:24

  Thank you very much, now it is more clear.

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