Glimmer Gene Prediction

Predict genes in microbial DNA with Glimmer

Glimmer Prediction Plugin

Glimmer (Gene Locator and Interpolated Markov ModelER) is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. Glimmer uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA.

Quick Start

Install the plugin by downloading the gplugin file and dragging it in to Geneious or use the plugin manager in Geneious (under Tools - Plugins in the menu).

Once installed, run the plugin by selecting a nucleotide sequence and choosing Annotate & Predict - Predict Genes with Glimmer from the menu. Results are saved as annotations on your sequence. Optionally a model can be pre-calculated from a sequence with annotated known genes using Annotate & Predict - Build Glimmer Gene Model from the menu.


1.5 (10 Mar 2017) – Download

– Fixed the plugin so it will work on Windows – Made it fail gracefully on training annotations that Glimmer is unable to process – Fixed cryptic failure messages on some sequences – Fixed a crash when the Glimmer model output contains an empty line

1.4 (07 Nov 2012) – Download

-Improved memory efficiency -Fixed parse error

1.3 (08 Jul 2011) – Download

Improved error handling to track down issues with Glimmer on certain data


Glimmer is an OSI Certified Open Source Software and is avaliable at


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