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ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences
Open accessAbstract
A computer program, ARAGORN, identifies tRNA and tmRNA genes. The program employs heuristic algorithms to predict tRNA secondary structure, based on homology with recognized tRNA consensus sequences and ability to form a base-paired cloverleaf. tmRNA genes are identified using a modified version of the BRUCE program. ARAGORN achieves a detection sensitivity of 99% from a set of 1290 eubacterial, eukaryotic and archaeal tRNA genes and detects all complete tmRNA sequences in the tmRNA database, improving on the performance of the BRUCE program. Recently discovered tmRNA genes in the chloroplasts of two species from the 'green' algae lineage are detected. The output of the program reports the proposed tRNA secondary structure and, for tmRNA genes, the secondary structure of the tRNA domain, the tmRNA gene sequence, the tag peptide and a list of organisms with matching tmRNA peptide tags.
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Cited by
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Brito, I. L., Yilmaz, S., Huang, K., Xu, L., Jupiter, S. D., Jenkins, A. P., Naisilisili, W., Tamminen, M., Smillie, C. S., Wortman, J. R., et al. (2016) · Nature · doi:10.1038/nature18927 · Cited by 288
“Metagenomic alignments were filtered for paired reads that had only one read-pair aligning to a horizontally transferred gene. tRNA genes were identified using the program ARAGORN 51 .”
Press, M. O., Wiser, A. H., Kronenberg, Z. N., Langford, K. W., Shakya, M., Lo, C.-C., Mueller, K. A., Sullivan, S. T., Chain, P. S. G., & Liachko, I. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/198713 · Cited by 103
Tamburini, F. B., Maghini, D., Oduaran, O. H., Brewster, R., Hulley, M. R., Sahibdeen, V., Norris, S. A., Tollman, S., Kahn, K., Wagner, R. G., et al. (2022) · Nature Communications · doi:10.1038/s41467-021-27917-x · Cited by 88
Calabrese, F. M., Ameur, H., Nikoloudaki, O., Celano, G., Vacca, M., Junior, W. J., Manzari, C., Vertè, F., Di Cagno, R., Pesole, G., et al. (2022) · Microbiome · doi:10.1186/s40168-022-01301-3 · Cited by 85
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“Briefly, ARA-GORN [45], Barrnap [46] and Prodigal [46] annotated the genes related to tRNA, rRNA and protein-coding sequences.”
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Di Pierro, F., Sagheddu, V., Galletti, S., Casaroli, A., Labrini, E., Soldi, S., Cazzaniga, M., Bertuccioli, A., Matera, M., Cavecchia, I., et al. (2026) · Probiotics and Antimicrobial Proteins · doi:10.1007/s12602-025-10522-5 · Cited by 5
“Coding sequences (CDS) were parsed with Prodigal [95], tRNAs were found using ARAGORN [96], and rRNAs were annotated using the Infernal command-line tools coupled with the HMM of the bacterial and archaeal rRNAs downloaded from RFAM [97].”
Bouderka, F., López-García, P., Deschamps, P., Zhou, Y., Krupovic, M., Gutiérrez-Preciado, A., Ciobanu, M., Bertolino, P., David, G., Moreira, D., et al. (2026) · mBio · doi:10.1128/mbio.00025-26 · Cited by 5
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Abedin, I., Putra, A., Kang, H.-E., Singh, A., Singh, S., Jung, W.-K., Kim, H.-W., & Kundu, S. (2025) · doi:10.21203/rs.3.rs-7140563/v1 · Cited by 1
Arnoux, J. (2026) · Thèse de doctorat, Université Paris-Saclay / PPanGGOLiN · doi:10.70675/eee354d9zf63dz48ebz9444zd1809f8fb74d
Genomic and structural insights into Jyvaskylavirus, the first giant virus isolated from Finland
Almeida, G. M. D. F., Arriaga, I., de Azevedo, B. L., Leppänen, M., Abrahão, J. S., Andreani, J., Zabeo, D., Ravantti, J. J., Abrescia, N. G., & Sundberg, L.-R. (2025) · eLife · doi:10.7554/elife.103492.3
Metadata
- Authors
- Laslett, D.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2004-01-02
- Volume
- 32
- Issue
- 1
- Pages
- 11-16
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W1996053875
- Cited by
- 2,705
- References
- 0
- FWCI
- 3.61
- Type
- journal article
- Language
- en
- Open access
- bronze
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