What training dataset was used for the NCBI Glimmer web server?

Question

[blrhgeruser1]

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?

[ojelizodun]

I have not been able to install GLIMMER on Windows 10. Please I need help on this. What I am trying to use it for is to check for the availability of some known genes like ArsD, ArsC and others in some bacteria genomes that I have downloaded their sequences in FASTA format. Please, I need enlightenment on how I can achieve this either with glimmer or using any other reliable protocol. Thank you.

[ATpoint]

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Answer 1

[Michael]

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