ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences.

By Dean Laslett, Björn Canbäck. Nucleic Acids Research, 2004

2,597 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/9a2fdaaa7166cfada4018f06e288df945f1136ce

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Citations in the corpus

Phage_Finder: Automated identification and classification of prophage regions in complete bacterial genome sequences (2006, methodology): “Phage_Finder was written in PERL (http://www.perl.org) and tested using PERL version 5.8.5+ on Linux and Mac OS X 10.3/10.4 operating systems, but should work in most Unix environments if the following helper programs are installed and functional: NCBI BLASTALL (13) or WUBLAST 2.0 (http://blast.wust”
PHAST: A Fast Phage Search Tool (2011, methodology): “Because tRNA and tmRNA sites provide valuable information for identifying the attachment sites, they are calculated using the programs tRNAscan-SE (15) and ARAGORN (16).”
Genome Sequencing and Comparative Transcriptomics of the Model Entomopathogenic Fungi Metarhizium anisopliae and M. acridum (2011, methodology): “Transfer RNAs (tRNAs) were predicted with tRNAscan-SE [114] and ARAGORN [115].”
Pharokka: a fast scalable bacteriophage annotation tool (2022, methodology): “In addition, Pharokka employs tRNAscan-SE 2 (Chan et al., 2021) to predict tRNAs, Aragorn (Laslett and Canback, 2004) to predict tmRNAs and MinCED to predict CRISPRs (Bland et al., 2007; Fig.”
tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes (2019, methodology): “Numerous other tRNA detection and classification methods have become available since tRNAscan-SE was first developed, including ARAGORN (6), which detects both tRNA genes and tmRNA genes; DOGMA (7), ARWEN (8), and MiTFi (9), which are designed for annotating tRNA genes in various types of organellar”
ICEberg 2.0: an updated database of bacterial integrative and conjugative elements (2018, methodology): “ICEfinder employs ARAGORN (21) with the default parameters to identify the 3′ termini of the tRNA/tmRNA genes as the putative ICE insertion sites.”
CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences (2012, methodology): “tRNA using ARAGORN, which has been shown to be able to recognize tRNA with introns in a reasonable amount of time [25].”
Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification (2021, methodology): “Furthermore, Bakta is available as a cloud-based web version for the convenient annotation of single genomes. tRNA and transfer- messenger-RNA (tmRNA) genes are predicted and annotated by tRNAscan-SE [18] and Aragorn [19], respectively.”
ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences (2008, methodology): “The precise scoring magnitudes and cut-off thresholds within each algorithm were calibrated manually to achieve maximum sensitivity using a training set of 125 annotated metazoan mitochondrial genomes with a total sequence length of 1.98 Megabases.”
Insights into Head-Tailed Viruses Infecting Extremely Halophilic Archaea (2013, background): “Finished sequences were analyzed and annotated with genome editors, including DNAMaster (http://cobamide2.bio.pitt.edu/), Glimmer (55), GeneMark (56), tRNA ScanSE (57), COILS (58), and Aragorn (59), to identify genome features.”
Query-Dependent Banding (QDB) for Faster RNA Similarity Searches (2007, background): “Weinberg Z, Ruzzo WL (2004) Exploiting conserved structure for faster annotation of non-coding RNAs without loss of accuracy.”