Glimmer statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Glimmer
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Tool usage distribution map

This map represents all the scientific publications referring to Glimmer per scientific context
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Protocols

Glimmer specifications

Information


Unique identifier OMICS_01486
Name Glimmer
Alternative name Glimmer3
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/GLIMMER

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Information


Unique identifier OMICS_01486
Name Glimmer
Alternative name Glimmer3
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/GLIMMER

Publications for Glimmer

Glimmer citations

 (1407)
library_books

Complete Genome Sequences of Bacillus Phages Janet and OTooleKemple52

2018
Genome Announc
PMCID: 5946042
PMID: 29748396
DOI: 10.1128/genomeA.00083-18

[…] 0-fold depth of coverage. Gene annotation was completed using DNA Master (see http://cobamide2.bio.pitt.edu/computer.htm), which includes the open reading frame (ORF) prediction tools GeneMark () and Glimmer () and the tRNA prediction tool ARAGORN (). Functional analysis was performed using BLASTp () and HHpred ().Janet has a length of 160,705 bp, with terminal repeats of 2,434 bp, while OTooleKem […]

call_split

Characterization and Genomic Study of Phage vB_EcoS B2 Infecting Multidrug Resistant Escherichia coli

2018
Front Microbiol
PMCID: 5945888
PMID: 29780362
DOI: 10.3389/fmicb.2018.00793
call_split See protocol

[…] Putative open reading frames (ORFs) were predicted using artemis software (http://www.sanger.ac.uk/science/tools/artemis) and Glimmer 3 (Aggarwal and Ramaswamy, ), with a threshold of 30 amino acids (aa) as a minimum for the length of protein. Function annotation was performed using the BLAST tools at NCBI (http://blast.ncbi […]

library_books

Elucidation of the anti hyperammonemic mechanism of Lactobacillus amylovorus JBD401 by comparative genomic analysis

2018
BMC Genomics
PMCID: 5918772
PMID: 29695242
DOI: 10.1186/s12864-018-4672-3

[…] r curated manually using web-based software and databases. FrameD [] was used for prediction of ORFs, and their starts were manually adjusted based on blast alignment. The gene model was predicted by Glimmer [] and compared with the following public databases: COGs [], Interpro [], Pfam [], Prints [], PROSITE [], Smart [], Swissprot [], and Tigrfams []. Tblastx [] was used to reanalyze intergenic […]

call_split

Complete Genome Sequence of the Heavy Metal Tolerant Endophytic Type Strain of Salinicola tamaricis

2018
Genome Announc
PMCID: 5908926
PMID: 29674561
DOI: 10.1128/genomeA.00358-18
call_split See protocol

[…] frequency, GC content, and genome coverage depth. This yielded a 4,276,240-bp genome sequence composed of 1 scaffold and 1 contig, with 65.68% GC content. The coding sequences were predicted by using Glimmer version 3.02 (). Functional annotation was achieved using databases, including Gene Ontology (GO) (), the Kyoto Encyclopedia of Genes and Genomes (KEGG) (, ), Swiss-Prot, the Cluster of Orthol […]

library_books

Complete Genome Sequence of the Poly γ Glutamate Synthesizing Bacterium Bacillus subtilis Bs 115

2018
Genome Announc
PMCID: 5908953
PMID: 29674533
DOI: 10.1128/genomeA.00197-18

[…] sists of a single circular chromosome of 4,142,593 bp and has an average GC content of 43.35%. There are a total of 4,661 putative open reading frames (with an average size of 792.91 bp) according to Glimmer (). Eighty-eight tRNA genes for all 20 amino acids and 10 16S-23S-5S rRNA operons were identified by tRNAscan-SE () and RNAmmer (), respectively.Sixteen simple sequence repeats (SSR) and 86 ta […]

library_books

Genome Sequences of Ilzat and Eleri, Two Phages Isolated Using Microbacterium foliorum NRRL B 24224

2018
Genome Announc
PMCID: 5897797
PMID: 29650566
DOI: 10.1128/genomeA.00144-18

[…] ly. The G+C contents of both phages are lower than that of the isolation host (68.7%; GenBank accession no. JYIU00000000).The genomes were annotated using DNA Master (http://cobamide2.bio.pitt.edu/), Glimmer (), GeneMark (), BLASTP (), HHpred (), and Phamerator (). A total of 62 and 63 protein-coding genes were identified in Ilzat and Eleri, respectively. The two phages share similar genome archit […]


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Glimmer institution(s)
Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, Department of Computer Science, University of Maryland, College Park, MD, USA

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