Glimmer specifications

Information


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

Glimmer article

Glimmer citations

 (12)
2017
PMCID: 5565763

[…] and the genome was assembled using soapdenovo v2.04 with all parameters set by default [12] and gapcloser v1.12 was used to fill local inner gaps. the open reading frames (orfs) were predicted using glimmer 3.02 [13]. the biological functions of these predicted orfs were annotated using various databases., the analyses of the assembled genome revealed a genome size of about 8,041,385 bp made […]

2017
PMCID: 5552980

[…] of 60.07% and comprising 73 contigs. scaffolding produced 60 supercontigs, of which the largest one (896,647 bp) represented 14.3% of the total assembly length. the genome was predicted using glimmer version 3.02; the chromosome contains 2 copies of rrnas, 61 trnas, and 5,672 protein-coding genes., the genome sequences have been deposited in ncbi genbank under the accession number […]

2017
PMCID: 5295034

[…] 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 […]

2016
PMCID: 4911491

[…] minimum sequence coverage of 50 times was obtained. genomes were assembled using gsassembler (v2.6) (roche applied science, indianapolis, in, usa), and open reading frames (orfs) were predicted with glimmer (v3.02) and manual annotations (8). homology and conserved domain searches were performed using blastp (http://blast.ncbi.nlm.nih.gov/blast.cgi), and the presence of trna sought […]

2016
PMCID: 4866403

[…] reagent kit v2.migs-29sequencing platformsillumina miseq systemmigs-31.2fold coverage634x chromosome, 691x plasmidmigs-30assemblersvelvet 1.2.10, geneious 7.1migs-32gene calling methodgeneious 7.1, glimmer 3.02, trnascan-selocus taghlasagenbank idcp011564 (chromosome)cp011565 (plasmid)genbank date of release30/09/2015bioprojectprjna284332migs-13source material identifierisolated […]

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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