Nucleic Acids Research, Vol 25, Issue 5 955-964, Copyright © 1997 by Oxford University Press
TM Lowe and SR Eddy
We describe a program, tRNAscan-SE, which identifies 99-100% of transfer
RNA genes in DNA sequence while giving less than one false positive per 15
gigabases. Two previously described tRNA detection programs are used as
fast, first-pass prefilters to identify candidate tRNAs, which are then
analyzed by a highly selective tRNA covariance model. This work represents
a practical application of RNA covariance models, which are general,
probabilistic secondary structure profiles based on stochastic context-free
grammars. tRNAscan-SE searches at approximately 30 000 bp/s. Additional
extensions to tRNAscan-SE detect unusual tRNA homologues such as
selenocysteine tRNAs, tRNA-derived repetitive elements and tRNA
pseudogenes.
ARTICLES
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence
Department of Genetics, Washington University School of Medicine, 660 South Euclid, Box 8232, St Louis, MO 63110, USA.
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D. C. S. G. Oliveira, R. Raychoudhury, D. V. Lavrov, and J. H. Werren Rapidly Evolving Mitochondrial Genome and Directional Selection in Mitochondrial Genes in the Parasitic Wasp Nasonia (Hymenoptera: Pteromalidae) Mol. Biol. Evol., October 1, 2008; 25(10): 2167 - 2180. [Abstract] [Full Text] [PDF]
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E. A. Welsh, M. Liberton, J. Stockel, T. Loh, T. Elvitigala, C. Wang, A. Wollam, R. S. Fulton, S. W. Clifton, J. M. Jacobs, et al. The genome of Cyanothece 51142, a unicellular diazotrophic cyanobacterium important in the marine nitrogen cycle PNAS, September 30, 2008; 105(39): 15094 - 15099. [Abstract] [Full Text] [PDF]
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J. Klumpp, J. Dorscht, R. Lurz, R. Bielmann, M. Wieland, M. Zimmer, R. Calendar, and M. J. Loessner The Terminally Redundant, Nonpermuted Genome of Listeria Bacteriophage A511: a Model for the SPO1-Like Myoviruses of Gram-Positive Bacteria J. Bacteriol., September 1, 2008; 190(17): 5753 - 5765. [Abstract] [Full Text] [PDF]
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L. Klasson, T. Walker, M. Sebaihia, M. J. Sanders, M. A. Quail, A. Lord, S. Sanders, J. Earl, S. L. O'Neill, N. Thomson, et al. Genome Evolution of Wolbachia Strain wPip from the Culex pipiens Group Mol. Biol. Evol., September 1, 2008; 25(9): 1877 - 1887. [Abstract] [Full Text] [PDF]
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M. A. Azcarate-Peril, E. Altermann, Y. J. Goh, R. Tallon, R. B. Sanozky-Dawes, E. A. Pfeiler, S. O'Flaherty, B. L. Buck, A. Dobson, T. Duong, et al. Analysis of the Genome Sequence of Lactobacillus gasseri ATCC 33323 Reveals the Molecular Basis of an Autochthonous Intestinal Organism Appl. Envir. Microbiol., August 1, 2008; 74(15): 4610 - 4625. [Abstract] [Full Text] [PDF]
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S. Sato, Y. Nakamura, T. Kaneko, E. Asamizu, T. Kato, M. Nakao, S. Sasamoto, A. Watanabe, A. Ono, K. Kawashima, et al. Genome Structure of the Legume, Lotus japonicus DNA Res, August 1, 2008; 15(4): 227 - 239. [Abstract] [Full Text] [PDF]
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M. Naito, H. Hirakawa, A. Yamashita, N. Ohara, M. Shoji, H. Yukitake, K. Nakayama, H. Toh, F. Yoshimura, S. Kuhara, et al. Determination of the Genome Sequence of Porphyromonas gingivalis Strain ATCC 33277 and Genomic Comparison with Strain W83 Revealed Extensive Genome Rearrangements in P. gingivalis DNA Res, August 1, 2008; 15(4): 215 - 225. [Abstract] [Full Text] [PDF]
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J. Uchiyama, M. Rashel, I. Takemura, H. Wakiguchi, and S. Matsuzaki In Silico and In Vivo Evaluation of Bacteriophage {phi}EF24C, a Candidate for Treatment of Enterococcus faecalis Infections Appl. Envir. Microbiol., July 1, 2008; 74(13): 4149 - 4163. [Abstract] [Full Text] [PDF]
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A. J. Heidel and G. Glockner Mitochondrial Genome Evolution in the Social Amoebae Mol. Biol. Evol., July 1, 2008; 25(7): 1440 - 1450. [Abstract] [Full Text] [PDF]
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H. Takarada, M. Sekine, H. Kosugi, Y. Matsuo, T. Fujisawa, S. Omata, E. Kishi, A. Shimizu, N. Tsukatani, S. Tanikawa, et al. Complete Genome Sequence of the Soil Actinomycete Kocuria rhizophila J. Bacteriol., June 15, 2008; 190(12): 4139 - 4146. [Abstract] [Full Text] [PDF]
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J. G. Elkins, M. Podar, D. E. Graham, K. S. Makarova, Y. Wolf, L. Randau, B. P. Hedlund, C. Brochier-Armanet, V. Kunin, I. Anderson, et al. A korarchaeal genome reveals insights into the evolution of the Archaea PNAS, June 10, 2008; 105(23): 8102 - 8107. [Abstract] [Full Text] [PDF]
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L. T. T. Tran-Nguyen, M. Kube, B. Schneider, R. Reinhardt, and K. S. Gibb Comparative Genome Analysis of "Candidatus Phytoplasma australiense" (Subgroup tuf-Australia I; rp-A) and "Ca. Phytoplasma asteris" Strains OY-M and AY-WB J. Bacteriol., June 1, 2008; 190(11): 3979 - 3991. [Abstract] [Full Text] [PDF]
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