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I am trying to find orfs with Glimmer. At the end, Glimmer gives me a .predict file with the orfs and a corresponding raw score.

When I look at the documentation, it says about the score, "This is 100 times the per-base log-odds ratio of the in-frame coding ICM score to the independent (i.e., non-coding) model score. It gives a rough quantification to how well an orf scores that can be compared between any two orfs." You can look here for the documentation-

https://ccb.jhu.edu/software/glimmer/glim302notes.pdf

But what does the score really mean in an absolute manner? How do I realize for an orf, if the score is significant or not?

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The score is the log odds ratio, times 100, that the ORF that you input is a coding region. For example, if Glimmer thinks the log odds are 10 to 1 that your region is coding, then your score will be 10x100 = 10000. Log odds of 10:1 imply more than a million to one certainty.

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    $\begingroup$ Thanks. But the documentation says log-odds ratio. But even then, my question is what is a good odds ratio absolutely. More abstractly, when can I be confident that this orf is really a coding region. $\endgroup$ – nafizh Aug 22 '16 at 21:45
  • $\begingroup$ You can't really be sure without experimentation and research, because glimmer can screw up. But a score of 300 or more suggests better than 90% odds that it is a coding region according to Glimmer. 10000+ implies a million to one odds. $\endgroup$ – D J Sims Aug 22 '16 at 21:50

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