Question: What training dataset was used for the NCBI Glimmer web server?
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gravatar for blrhgeruser1
4.3 years ago by
blrhgeruser140
United States
blrhgeruser140 wrote:

I am trying to recreate the results from NCBI's web server for Glimmer: http://www.ncbi.nlm.nih.gov/genomes/MICROBES/glimmer_3.cgi

However, I don't see any information on what training datasets they used and what options are being passed to Glimmer, other than that selecting a linear topology probably passes the "-l" option. Can anyone help?

glimmer gene finding ncbi • 1.5k views
ADD COMMENTlink modified 3.3 years ago by Michael Dondrup45k • written 4.3 years ago by blrhgeruser140
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gravatar for Michael Dondrup
3.3 years ago by
Bergen, Norway
Michael Dondrup45k wrote:

The training set for glimmer is often derived from long non-overlapping ORFs >500bp from the same genome. This is the 'default' way of deriving a training set for glimmer and was possibly used by ncbi. The training method is described in the glimmer paper http://nar.oxfordjournals.org/content/27/23/4636.long

ADD COMMENTlink written 3.3 years ago by Michael Dondrup45k
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