Question: What training dataset was used for the NCBI Glimmer web server?
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gravatar for blrhgeruser1
4.4 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 • 1.6k views
ADD COMMENTlink modified 27 days ago by ojelizodun0 • written 4.4 years ago by blrhgeruser140

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.

ADD REPLYlink written 27 days ago by ojelizodun0

You've already been asked (A: How do I use Glimmer 3.02?) not to use the answer field in old threads to ask questions. Please follow the community rules and open a new question in case of problems. Please make sure to first read and follow Brief Reminder On How To Ask A Good Question to increase your changes of a good answer.

ADD REPLYlink written 27 days ago by ATpoint13k
0
gravatar for Michael Dondrup
3.5 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 3.5 years ago by Michael Dondrup45k
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