Using Glimmer on HPC

Glimmer comes with the Rocks Bio Roll's standard brief documentation, but much more information is available in the Release Notes. Glimmer uses interpolated Markov models (IMMs) in a two step process that first trains the model on similar species' genomes, and then discovers the most probable instances of that model on query sequences. The path to Glimmer, /opt/Bio/glimmer/bin, is assigned by activating the Bio Roll, and use the following command to see all of its options:

glimmer3 -h

There are sample runs in /opt/Bio/glimmer/bin/sample-run and sample scripts in /opt/Bio/glimmer/bin/scripts.