Glimmer protocols

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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 in pipelines

 (377)
2018
PMCID: 5764923
PMID: 29326199
DOI: 10.1128/genomeA.01101-17

[…] segment of tortellini has diverged considerably from subcluster p1 phages, the p1 phages have extensive sequence similarity to cluster i phages in this region (). genomes were auto-annotated using glimmer () and genemark () and refined by manual inspection; the number of protein-coding genes ranges from 76 to 81 (). functions were assigned using phamerator (), blastp (), and hhpred (). […]

2018
PMCID: 5764924
PMID: 29326200
DOI: 10.1128/genomeA.01143-17

[…] reads (1,583,977,748 bp) were trimmed and assembled using clc genomics workbench version 6.5.1 (qiagen, netherlands). open reading frame (orf) prediction and annotation were conducted using glimmer version 3.02 (), prodigal version 1.20 (), genemarks version 4.08 (), and protein blast () and confirmed by the rapid annotations using subsystems technology (rast) version 2.0 server (). […]

2018
PMCID: 5764925
PMID: 29326201
DOI: 10.1128/genomeA.01146-17

[…] in subcluster be1; mildred21 is the least similar to other be1 phages. electron microscopy shows these phages to have a siphoviral morphology and isometric capsids., all genomes were annotated using glimmer and genemarks and refined using blast alignments to previous manually annotated genes; start codon choice was evaluated using multiple sequence alignments of closely related genes. putative […]

2018
PMCID: 5786693
PMID: 29371367
DOI: 10.1128/genomeA.01555-17

[…] microscopy showed that demsculpinboyz belongs to the siphoviridae family and has a short tail with an icosahedral capsid., protein-coding genes in the genome were autoannotated and identified using glimmer and genemark, proceeded by manual inspection and annotation editing. a total of 116 protein-coding genes were predicted, making up 94.75% of the genome coding capacity. this genome contains […]

2018
PMCID: 5805866
PMID: 29439028
DOI: 10.1128/genomeA.00002-18

[…] gapcloser version 1.12 ()., the assembled draft genome contained 4,710,590 bp in 56 contigs with an average of 20× coverage and 31.2% g+c content. the open reading frames (orfs) were analyzed using glimmer 3.02 (), and all predicted orfs were then searched by blast against all proteins from complete microbial genomes by using the ncbi prokaryotic genome annotation pipeline (). trnascan-se […]


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Glimmer in publications

 (1424)
PMCID: 5946042
PMID: 29748396
DOI: 10.1128/genomeA.00083-18

[…] 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, […]

PMCID: 5945888
PMID: 29780362
DOI: 10.3389/fmicb.2018.00793

[…] into a whole genome using soapdenovov2.04 software and gapcloserv1.12., 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 […]

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

[…] of 1,946,267 bp with an average gc content of 38.13%. the complete genome sequence was deposited in the genbank database (accession no. cp012389). the genome contained 2244 orfs predicted by glimmer, but manual annotation resulted in 1979 protein encoding genes, representing a coding density of 84.17%. seven rrnas (consisting of 5 s, 16s, and 23s), one non-coding rna, and 35 trnas […]

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

[…] 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 […]

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

[…] 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 […]


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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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