Glimmer

Software Category
Version
3.02b

Glimmer

Glimmer is a set of bioinformatics programs designed primarily for use with microbial genomic data sets. It is designed to find genes and separate out coding regions from non-coding regions in these datasets using an Interpolated Markov Model approach.

Using Glimmer on RCC Resources

Running Glimmer Sequentially on HPC

Glimmer's program set requires the gnu module to be run on HPC login nodes. There are numerous commands available within Glimmer. For a complete list and usage documentation, please refer to the official website, as there are release notes available there for this purpose. In order to run a command like glimmer3 on HPC, simply run the commands:

module load gnu
glimmer3 -[OPTIONS] SEQ_FILE ICM_FILE OUTPUT

In the example above, there are a long list of options available with the glimmer3 command. The SEQ_FILE argument should be a genetic sequence file and the ICM_FILE is an Interpolated Context Model file which is required for Glimmer's program.

If you do not have a pre-made ICM file, one can be generated from training sequences using the build-icm command. Note that the build-icm command may require you to specify the entire path to the build-icm executable which is /opt/rcc/gnu/libexec/glimmer3/build-icm [OPTS] FILE. Detailed usage documentation on this and all other component programs can be found in the release notes on the official website.

Two output options are available. You can request a .detail file for details and a .predict file for model predictions. The OUTPUT argument should be the name of the file you want to send the output to.