GLIMMER

In bioinformatics, GLIMMER (Gene Locator and Interpolated Markov ModelER) is used to find genes in prokaryotic DNA. "It is effective at finding genes in bacteria, archea, viruses, typically finding 98-99% of all relatively long protein coding genes". GLIMMER was the first system that used the interpolated Markov model to identify coding regions. The GLIMMER software is open source and is maintained by Steven Salzberg, Art Delcher, and their colleagues at the Center for Computational Biology at Johns Hopkins University. The original GLIMMER algorithms and software were designed by Art Delcher, Simon Kasif and Steven Salzberg and applied to bacterial genome annotation in collaboration with Owen White.

First Version of GLIMMER "i.e., GLIMMER 1.0" was released in 1998 and it was published in the paper Microbial gene identification using interpolated Markov model. Markov models were used to identify microbial genes in GLIMMER 1.0. GLIMMER considers the local composition sequence dependencies which makes GLIMMER more flexible and more powerful when compared to fixed-order Markov model.

There was a comparison made between interpolated Markov model used by GLIMMER and fifth order Markov model in the paper Microbial gene identification using interpolated Markov models. "GLIMMER algorithm found 1680 genes out of 1717 annotated genes in Haemophilus influenzae where fifth order Markov model found 1574 genes. GLIMMER found 209 additional genes which were not included in 1717 annotated genes where fifth order Markov model found 104 genes."'

Second Version of GLIMMER i.e., GLIMMER 2.0 was released in 1999 and it was published in the paper Improved microbial identification with GLIMMER. This paper provides significant technical improvements such as using interpolated context model instead of interpolated Markov model and resolving overlapping genes which improves the accuracy of GLIMMER.