tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
Todd M. Lowe,Sean R. Eddy +1 more
TLDR
A program is described, tRNAscan-SE, which identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases.Abstract:
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.read more
Citations
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Ma-LMM01 Infecting Toxic Microcystis aeruginosa Illuminates Diverse Cyanophage Genome Strategies
Takashi Yoshida,Keizo Nagasaki,Yukari Takashima,Yoko Shirai,Yuji Tomaru,Yoshitake Takao,Shigetaka Sakamoto,Shingo Hiroishi,Hiroyuki Ogata +8 more
TL;DR: The first sequenced freshwater cyanomyovirus genome of Ma-LMM01 is described, indicating that it is a member of a new lineage of the Myoviridae family and light is central in the phage-cyanobacterium relationships where the viruses use diverse genetic strategies to control their host's photosynthesis.
Journal ArticleDOI
Genome Comparison of Pseudomonas aeruginosa Large Phages
Kirsten Hertveldt,Rob Lavigne,E. A. Pleteneva,Natalia V. Sernova,Lidia P. Kurochkina,Roman Korchevskii,Johan Robben,Vadim V. Mesyanzhinov,Victor N. Krylov,Guido Volckaert +9 more
TL;DR: Comparative EL and phiKZ genomics reveals that these giant phages are an example of substantially diverged genetic mosaics, and five genome regions can be delineated in EL.
Journal ArticleDOI
Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans.
TL;DR: It is proposed that nematode genomes contain an alternative set of CNEs that share sequence characteristics, but not identity, with their vertebrate counterparts, and reflect the parallel evolution of alternative enhancers for a common set of developmental regulatory genes in different animal groups.
Journal ArticleDOI
Evidence for reductive genome evolution and lateral acquisition of virulence functions in two Corynebacterium pseudotuberculosis strains.
Jeronimo C. Ruiz,Vivian D'Afonseca,Artur Silva,Amjad Ali,Anne Cybelle Pinto,Anderson Rodrigues dos Santos,Aryanne A. M. C. Rocha,Débora de Oliveira Lopes,Fernanda Alves Dorella,Luis G.C. Pacheco,Luis G.C. Pacheco,Marcília P. Costa,Meritxell Zurita Turk,Núbia Seyffert,Pablo M. R. O. Moraes,Siomar de Castro Soares,Sintia Almeida,Thiago Luiz de Paula Castro,Vinicius A. C. Abreu,Eva Trost,Jan Baumbach,Andreas Tauch,Maria Paula Cruz Schneider,John A. McCulloch,Louise Cerdeira,Rommel Thiago Jucá Ramos,Adhemar Zerlotini,Anderson J. Dominitini,Daniela de Melo Resende,Daniela de Melo Resende,Elisângela Monteiro Coser,Luciana M. Oliveira,André Luiz Pedrosa,Carlos Ueira Vieira,Claudia Teixeira Guimarães,Daniela C. Bartholomeu,Diana Oliveira,Fabrício R. Santos,Élida Mara Leite Rabelo,Francisco Pereira Lobo,Glória Regina Franco,Ana Flávia D.V. Costa,Ieso de Miranda Castro,Sílvia Regina Costa Dias,Jesus Aparecido Ferro,José Miguel Ortega,Luciano Vilela Paiva,Luiz Ricardo Goulart,Juliana Franco Almeida,Maria Inês Tiraboschi Ferro,Newton Portilho Carneiro,Paula R. K. Falcão,Priscila Grynberg,Santuza M. R. Teixeira,Sérgio Hermínio Brommonschenkel,Sergio C. Oliveira,Roberto Meyer,Robert J. Moore,Anderson Miyoshi,Guilherme Oliveira,Guilherme Oliveira,Vasco Azevedo +61 more
TL;DR: These particular genome characteristics of C. pseudotuberculosis, as well as its acquired virulence factors in pathogenicity islands, provide evidence of its lifestyle and of the pathogenic pathways used by this pathogen in the infection process.
Journal ArticleDOI
Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria
György Sipos,Arun N. Prasanna,Mathias C. Walter,Eoin O’Connor,Balázs Bálint,Krisztina Krizsán,Brigitta Kiss,Jaqueline Hess,Torda Varga,Jason C. Slot,Robert Riley,Bettina Bóka,Daniel Rigling,Kerrie Barry,Juna Lee,Sirma Mihaltcheva,Kurt LaButti,Anna Lipzen,Rose Waldron,Nicola M. Moloney,Christoph Sperisen,László Kredics,Csaba Vágvölgyi,Andrea Patrignani,David A. Fitzpatrick,István Nagy,Sean Doyle,James B. Anderson,Igor V. Grigoriev,Ulrich Güldener,Martin Münsterkötter,László Nagy +31 more
TL;DR: The results suggest that the evolution of the unique dispersal and pathogenicity mechanisms of Armillaria might have drawn upon ancestral genetic toolkits for wood-decay, morphogenesis and complex multicellularity.
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