In bioinformatics GLIMMER (Gene Locator and Interpolated Markov ModelER) was the first system for finding genes that used the interpolated Markov model formalism. It is 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 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. (2006) examined the gene finding methods used for 183 genomes. They reported 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. It is also being used by this group to annotate viruses. 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 a highly cited bioinformatics system in the scientific literature. According to Google Scholar, as of early 2011 the original Glimmer article (Salzberg et al., 1998) has been cited 581 times, and the Glimmer 2.0 article (Delcher et al., 1999) has been cited 950 times.
Famous quotes containing the word glimmer:
“If you stand right fronting and face to face to a fact, you will see the sun glimmer on both its surfaces, as if it were a cimeter, and feel its sweet edge dividing you through the heart and marrow, and so you will happily conclude your mortal career. Be it life or death, we crave only reality. If we are really dying, let us hear the rattle in our throats and feel cold in the extremities; if we are alive, let us go about our business.”
—Henry David Thoreau (1817–1862)
“Nothing ... is so ungrateful as a rising generation; yet, if there is any faintest glimmer of light ahead of us in the present, it was kindled by the intellectual fires that burned long before us.”
—Ellen Glasgow (1873–1945)
“This, our respectable daily life, on which the man of common sense, the Englishman of the world, stands so squarely, and on which our institutions are founded, is in fact the veriest illusion, and will vanish like the baseless fabric of a vision; but that faint glimmer of reality which sometimes illuminates the darkness of daylight for all men, reveals something more solid and enduring than adamant, which is in fact the cornerstone of the world.”
—Henry David Thoreau (1817–1862)