GLIMMER: Difference between revisions
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{{Infobox Software |
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| name = GLIMMER |
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| developer = Steven Salzberg & Art Delcher |
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| latest_release_version = 3.02 |
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| latest_release_date = {{release date|2006|05|09|df=yes}} |
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| programming language = |
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| language = |
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| genre = [[Bioinformatics]] tool |
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| license = OSI Certified Open Source Software under the Artistic License |
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| website = {{URL|http://www.cbcb.umd.edu/software/glimmer/}} |
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}} |
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In [[bioinformatics]] '''GLIMMER (Gene Locator and Interpolated Markov ModelER)''' was the first system for [[gene prediction|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''<ref>{{cite web|title=Center for Bioinformatics and Computational Biology|url=http://cbcb.umd.edu/|publisher=University of Maryland|accessdate=23 March 2012}}</ref> at the [[University of Maryland, College Park]]. |
In [[bioinformatics]] '''GLIMMER (Gene Locator and Interpolated Markov ModelER)''' was the first system for [[gene prediction|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''<ref>{{cite web|title=Center for Bioinformatics and Computational Biology|url=http://cbcb.umd.edu/|publisher=University of Maryland|accessdate=23 March 2012}}</ref> at the [[University of Maryland, College Park]]. |
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Revision as of 14:03, 23 March 2012
| Developer(s) | Steven Salzberg & Art Delcher |
|---|---|
| Stable release | 3.02
/ 9 May 2006 |
| Type | Bioinformatics tool |
| License | OSI Certified Open Source Software under the Artistic License |
| Website | www |
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[1] 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)[2] 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.[3] It is also being used by this group to annotate viruses.[4] Glimmer is part of the bacterial annotation pipeline at the National Center for Biotechnology Information (NCB),[5] which also maintains a web server for Glimmer,[6] as do sites in Germany,[7] Canada,[8] 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)[9] has been cited 581 times, and the Glimmer 2.0 article (Delcher et al., 1999)[10] has been cited 950 times.
References
- ^ "Center for Bioinformatics and Computational Biology". University of Maryland. Retrieved 23 March 2012.
- ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 17166861, please use {{cite journal}} with
|pmid=17166861instead. - ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 17108353, please use {{cite journal}} with
|pmid=17108353instead. - ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 17158166, please use {{cite journal}} with
|pmid=17158166instead. - ^ "NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP)". Center for Bioinformatics and Computational Biology. Retrieved 23 March 2012.
- ^ "Microbial Genome Annotation Tools". Center for Bioinformatics and Computational Biology. Retrieved 23 March 2012.
- ^ "TiCo". Institut für Mikrobiologie und Genetik, Universität Göttingen. Retrieved 23 March 2012.
- ^ "BASys Bacterial Annotation System". Retrieved 23 March 2012.
- ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 9421513, please use {{cite journal}} with
|pmid=9421513instead. - ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 10556321, please use {{cite journal}} with
|pmid=10556321instead.
External links
- The Glimmer home page, from which the software can be downloaded.