ARAGORN protocols

ARAGORN specifications

Information


Unique identifier OMICS_04227
Name ARAGORN
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Information


Unique identifier OMICS_04227
Name ARAGORN
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for ARAGORN

ARAGORN IN pipelines

 (5)
2018
PMCID: 5908940
PMID: 29674547
DOI: 10.1128/genomeA.00287-18

[…] sequences covered most of the coding regions., annotation of the genome sequence using the rapid annotations using subsystem technology (rast) server (5), followed by trna and rrna detection using aragorn (6) and rnammer (7), respectively, identified 5,528 coding sequences, 79 trnas, and 9 rrnas in p. coffeiphila 342 and 5,998 coding sequences, 77 trnas, and 11 rrnas in pseudomonas sp. 382., […]

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

[…] 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, while otoolekemple52 (otk52) has a genome length […]

2014
PMCID: 4149004
PMID: 25197448
DOI: 10.4056/sigs.4778605

[…] [3] using mauve [38-40]., protein-coding genes (orfs) of draft genome assemblies were predicted using glimmer version 3.02 with a self-training dataset [41,42]. trnas and rrnas were predicted using aragorn and rnammer, respectively [43,44]. functional assignments of the predicted orfs were based on a blastp homology search against two genome sequences, g. thailandicus nbrc 3255 and g. oxydans […]

2013
PMCID: 3668014
PMID: 23723406
DOI: 10.1128/genomeA.00311-13

[…] of 2,772,624 bp with 41.6% g+c content and an n50 length of 134,259 bp. protein-coding gene prediction was performed by glimmer 3.02 with a self-training dataset (6). trnas were predicted using aragorn (7). functional annotation of the predicted genes was performed by blastp searching of the nr database (8). the draft genome sequence of a. flavothermus contains 90 contigs, including 52 […]

2013
PMCID: 3772147
PMID: 24029763
DOI: 10.1128/genomeA.00717-13

[…] (n50, 45 kb) were further validated (paired-end criterion) using bwa-0.5.9 (6). glimmer-3.02 (7) was used to predict the protein-encoding genes, whereas trna and rrna genes were identified using aragorn (8) and rnammer (9), respectively. a total of 4,033 coding sequences (cds), 70 pseudogenes, 54 trna genes, and 1 rrna operon were observed, with an average g+c content of 64%. validated […]

ARAGORN institution(s)
Murdoch University, Perth, Western Australia, Australia; Department of Microbial Ecology, Ecology Building, Lund University, Sweden

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