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HandWiki. GLIMMER. Encyclopedia. Available online: https://encyclopedia.pub/entry/34046 (accessed on 13 September 2026).
HandWiki. GLIMMER. Encyclopedia. Available at: https://encyclopedia.pub/entry/34046. Accessed September 13, 2026.
HandWiki. "GLIMMER" Encyclopedia, https://encyclopedia.pub/entry/34046 (accessed September 13, 2026).
HandWiki. (2022, November 11). GLIMMER. In Encyclopedia. https://encyclopedia.pub/entry/34046
HandWiki. "GLIMMER." Encyclopedia. Web. 11 November, 2022.
GLIMMER
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The content is sourced from: https://handwiki.org/wiki/Software: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.

glimmer bioinformatics bacterial genome

References

  1. Salzberg, S. L.; Delcher, A. L.; Kasif, S.; White, O. (1998). "Microbial gene identification using interpolated Markov models". Nucleic Acids Research 26 (2): 544–548. doi:10.1093/nar/26.2.544. PMID 9421513.  http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=147303
  2. Delcher, A.; Harmon, D.; Kasif, S.; White, O.; Salzberg, S. (1999). "Improved microbial gene identification with GLIMMER". Nucleic Acids Research 27 (23): 4636–4641. doi:10.1093/nar/27.23.4636. PMID 10556321.  http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=148753
  3. Delcher, A. L.; Bratke, K. A.; Powers, E. C.; Salzberg, S. L. (2007). "Identifying bacterial genes and endosymbiont DNA with Glimmer". Bioinformatics 23 (6): 673–679. doi:10.1093/bioinformatics/btm009. PMID 17237039.  http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2387122
  4. Kosuge, T.; Abe, T.; Okido, T.; Tanaka, N.; Hirahata, M.; Maruyama, Y.; Mashima, J.; Tomiki, A. et al. (2006). "Exploration and Grading of Possible Genes from 183 Bacterial Strains by a Common Protocol to Identification of New Genes: Gene Trek in Prokaryote Space (GTPS)". DNA Research 13 (6): 245–254. doi:10.1093/dnares/dsl014. PMID 17166861.  https://dx.doi.org/10.1093%2Fdnares%2Fdsl014
  5. Sugawara, H.; Abe, T.; Gojobori, T.; Tateno, Y. (2007). "DDBJ working on evaluation and classification of bacterial genes in INSDC". Nucleic Acids Research 35 (Database issue): D13–D15. doi:10.1093/nar/gkl908. PMID 17108353.  http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1669713
  6. Hirahata, M.; Abe, T.; Tanaka, N.; Kuwana, Y.; Shigemoto, Y.; Miyazaki, S.; Suzuki, Y.; Sugawara, H. (2007). "Genome Information Broker for Viruses (GIB-V): Database for comparative analysis of virus genomes". Nucleic Acids Research 35 (Database issue): D339–D342. doi:10.1093/nar/gkl1004. PMID 17158166.  http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1781101
  7. "NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP)". Center for Bioinformatics and Computational Biology. https://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html. Retrieved 23 March 2012. 
  8. "Microbial Genome Annotation Tools". Center for Bioinformatics and Computational Biology. https://www.ncbi.nlm.nih.gov/genomes/MICROBES/glimmer_3.cgi. Retrieved 23 March 2012. 
  9. "TiCo". Institut für Mikrobiologie und Genetik, Universität Göttingen. 2005-02-11. http://tico.gobics.de. Retrieved 23 March 2012. 
  10. "BASys Bacterial Annotation System". Archived from the original on 24 July 2012. https://web.archive.org/web/20120724072849/http://basys.ca/basys/cgi/submit.pl. Retrieved 23 March 2012. 
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