Monday, 5 September 2011


GLIMMER (Gene Locator and Interpolated Markov ModelER) was the first bioinformatics system for finding genes that used the interpolated Markov model formalism. It is very effective at finding genes in bacteria, archaea, and viruses, typically finding 98–99% of all protein-coding genes. The GLIMMER software is open source and can be found at the links below. It is maintained by Steven Salzberg, Art Delcher, and their colleagues at the Center for Bioinformatics and Computational Biology at the University of Maryland, College Park.

Because of its exceptionally high accuracy, Glimmer is the system of choice for genome annotation efforts on a wide range of bacteria, archaeal, and viral species. In a large-scale reannotation effort at the DNA Data Bank of Japan (DDBJ, which mirrors Genbank), Kosuge et al. (Kosuge et al. 2006) examined the gene finding methods used for 183 genomes. They report that of these projects, Glimmer was the gene finder for 49%, followed by Genemark with 12%, with other algorithms used in 3% or fewer of the projects. (They also reported that 33% of genomes used “other” programs, which in many cases meant that they could not identify the method. Excluding those cases, Glimmer was used for 73% of the genomes for which the methods could be unambiguously identified.) Glimmer was used by the DNA Databank of Japan (DDBJ) to re-annotate all bacterial genomes in the International Nucleotide Sequence Databases (Sugawara et al. 2007). It is also being used by this group to annotate viruses (Hirahata et al. 2007). Glimmer is part of the bacterial annotation pipeline at the National Center for Biotechnology Information (NCB))

(, which also maintains a web server for Glimmer (, as do sites in Germany (, Canada (, and elsewhere.
Glimmer is one of the most highly cited bioinformatics systems in the scientific literature. According to Google Scholar, as of early 2011 the original (Salzberg et al., 1998) Glimmer article has been cited 581 times and the Glimmer 2.0 article (Delcher et al., 1999) has been cited 950 times.