Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. Glimmer, Gene Locator and Interpolated Markov ModelER, uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. The IMM approach uses a combination of Markov models from 1st through 8th-order, weighting each model according to its predictive power. Glimmer uses 3-periodic nonhomogenous Markov models in its IMMs.


Glimmer3 is presented as a suite of programs that can be used independently:

identifies long, non-overlapping open reading frames (ORFs) in a DNA sequence file.
reads FASTA-format sequence-file and extract from it the subsequences specified by coords.
produces a probability model of coding sequences, called an interpolated context model or ICM.
reads DNA sequences in sequence-file and predict genes in them using the Interpolated Context Model. Outputs are a detail file and a prediction file.
reads DNA sequence in sequence-file and for each region specified by the coordinates in coords, check whether the region represents a normal gene, i.e., it begins with a start codon, ends with a stop codon, and has no frame shifts.


Identifying bacterial genes and endosymbiont DNA with Glimmer.
A.L. Delcher, K.A. Bratke, E.C. Powers and S.L. Salzberg.
Bioinformatics 23 (6): 673-679.