Glimmer
Encyclopedia
GLIMMER 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)) (http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html), which also maintains a web server for Glimmer (http://www.ncbi.nlm.nih.gov/genomes/microbes/glimmer_3.cgi), as do sites in Germany (http://tico.gobics.de/), Canada (http://wishart.biology.ualberta.ca/basys), 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.
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
system for finding genes
Gene prediction
In computational biology gene prediction or gene finding refers to the process of identifying the regions of genomic DNA that encode genes. This includes protein-coding genes as well as RNA genes, but may also include prediction of other functional elements such as regulatory regions...
that used the interpolated Markov model
Markov model
In probability theory, a Markov model is a stochastic model that assumes the Markov property. Generally, this assumption enables reasoning and computation with the model that would otherwise be intractable.-Introduction:...
formalism. It is very effective at finding genes in bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
, archaea
Archaea
The Archaea are a group of single-celled microorganisms. A single individual or species from this domain is called an archaeon...
, 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
Steven Salzberg
Steven Salzberg is an American Biologist and Computer Scientist who since 2011 has been a Professor of Medicine and Biostatistics in the Institute of Genetic Medicine at Johns Hopkins School of Medicine...
, Art Delcher, and their colleagues at the Center for Bioinformatics and Computational Biology at the University of Maryland, College Park
University of Maryland, College Park
The University of Maryland, College Park is a top-ranked public research university located in the city of College Park in Prince George's County, Maryland, just outside Washington, D.C...
.
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
GenBank
The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. This database is produced and maintained by the National Center for Biotechnology Information as part of the International Nucleotide Sequence...
), 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)) (http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html), which also maintains a web server for Glimmer (http://www.ncbi.nlm.nih.gov/genomes/microbes/glimmer_3.cgi), as do sites in Germany (http://tico.gobics.de/), Canada (http://wishart.biology.ualberta.ca/basys), 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.
External links
- The Glimmer home page, from which the software can be downloaded.