Glimmer 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 IN pipelines

 (85)
2018
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 (2) and glimmer (3) and the trna prediction tool aragorn (4). functional analysis was performed using blastp (5) and hhpred (6)., janet has a length of 160,705 bp, with terminal repeats of 2,434 bp, […]

2017
PMCID: 5295034
PMID: 28106814
DOI: 10.3390/genes8010040

[…] coverage for the sequence is 19.56. the sequence of the aquamicrobium phage p14 genome was deposited in the ncbi genbank database [27], accession: kx660669., the reading frames were located using glimmer 3.0 [28]. the genes were then identified using ncbi blastx [29] and searching the non-redundant protein sequences database. for the search the default settings were used (blosum62 matrix, gap […]

2017
PMCID: 5331496
PMID: 28183756
DOI: 10.1128/genomeA.01559-16

[…] illumina technology. the genome was assembled using spades (9) and edena (10) software, and multiplex pcr was used to close the gaps and remove regions of low coverage (11). the software program glimmer (12) and the rast suite (13) were used to identify protein-coding genes and for gene annotation, respectively., the complete genome of strain l. plantarum cgmcc 8198 contains a single […]

2017
PMCID: 5378303
PMID: 28099413
DOI: 10.1038/nature21049

[…] that were further manually assembled based on end-homologies. assembled genome was permuted to conform with the spbeta phage genome coordinates (accession nc_001884). orfs were predicted using glimmer29 with options -o50 -g110 -t30, and products were assigned to the orfs using rpsblast against the conserved domain database (cdd) version 3.12 with e-value of 1e-05. intergenic regions […]

2017
PMCID: 5399248
PMID: 28428289
DOI: 10.1128/genomeA.00153-17

[…] (n50, 133,347 bp; largest contig, 294,260 bp) with an average coverage of 90×. the draft genome of methylocaldum sp. 14b is 4,820,475 bp, with a g+c content of 58.24%. genes were predicted using glimmer 3.02 (5–7), and only open reading frames (orfs) longer than 100 amino acid residues were considered genes. genes were annotated using the ncbi nr, kegg (8–11), cog (11, 12), swiss-prot (13), […]

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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