NCBI GLIMMER Microbial Genome Annotation Tool

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



It is an online tool although it can be easily be downloadable as a software to analyze transcription units and open reading frames in both the strands of the DNA.

The online link for GLIMMER:


GLIMMER allows to find identification ~97-98% of the subject genes compared with the published annotation. GLIMMER is known to have <1% less accuracy.

The computational methods behind the GLIMMER Technique can be found at


To Start with GLIMMER:

After you go the NCBI’s GLIMMER you can able to download the GLIMMER software or you can choose the online program to feed your FASTA sequence of the gene from the unknown bacteria. (You can try with the FASTA sequence of any known bacteria).


Some additional parameters you need to maintain like the genetic code and the topology of the gene and then you can Run GLIMMER v3.02



After you Run GLIMMER you will get the following result as for example.



The result you get shows the number of ORFs or the open reading frames in the gene followed by the nucleotide starting number from where the ORF starts and then the nucleotide end number where the ORF ends. Minus (-) and plus (+) signifies the Lagging and the Leading strands respectively.

GLIMMER is quite efficient and can be useful for the microbial genetics studies. Read more about GLIMMER at


About Saumyadip

Science Communicator and Biologist. Keep interests in host-pathogen interaction research. Specifically bacterial infection mechanism, host infection evasion and immune susceptibility of host. PhD student at Academia Sinica Molecular and Cell Biology, Taiwan
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