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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Novel protein genes in animal mtDNA: a new sex determination system in freshwater mussels (Bivalvia: Unionoida)?
Sophie Breton,Donald T. Stewart,Sally Shepardson,R.J. Trdan,Arthur E. Bogan,Eric G. Chapman,Andrew J. Ruminas,Helen Piontkivska,Walter R. Hoeh +8 more
TL;DR: It is shown that mtDNA intraorganismal heteroplasmy can have deterministic underpinnings and persist for hundreds of millions of years and support the hypothesis that proteins coded by the highly divergent maternally and paternally transmitted mt genomes could be directly involved in sex determination in freshwater mussels.
Journal ArticleDOI
Genome Comparison of Barley and Maize Smut Fungi Reveals Targeted Loss of RNA Silencing Components and Species-Specific Presence of Transposable Elements
John D. Laurie,Shawkat Ali,Rob Linning,Gertrud Mannhaupt,Philip C. Wong,Ulrich Güldener,Martin Münsterkötter,Richard A. Moore,Regine Kahmann,Guus Bakkeren,Jan Schirawski,Jan Schirawski +11 more
TL;DR: Evidence of repeat-induced point mutations in the genome of U. hordei is found, indicating that smut fungi use different strategies to counteract the deleterious effects of repetitive DNA.
Journal ArticleDOI
The ICESt1 element of Streptococcus thermophilus belongs to a large family of integrative and conjugative elements that exchange modules and change their specificity of integration.
TL;DR: It is proposed to call all the conjugative elements that excise by site-specific recombination and integrate by recombination between a specific site of a circular intermediate and another site, "Integrative and Conjugative Elements" (ICEs), irrespective of the integration specificity.
Journal ArticleDOI
The Complete Genome Sequence of Thermococcus onnurineus NA1 Reveals a Mixed Heterotrophic and Carboxydotrophic Metabolism
Hyun Sook Lee,Sung Gyun Kang,Seung Seob Bae,Jae Kyu Lim,Yona Cho,Yun Jae Kim,Jeong Ho Jeon,Sun Shin Cha,Kae Kyoung Kwon,Hyungtae Kim,Cheol-Joo Park,Heewook Lee,Seung Il Kim,Jongsik Chun,Rita R. Colwell,Sang-Jin Kim,Jung-Hyun Lee +16 more
TL;DR: The complete genome sequence and feature analysis of Thermococcus onnurineus NA1 isolated from a deep-sea hydrothermal vent area reveals clues to its physiology, providing the first genomic evidence for the carboxydotrophy in Thermitis.
Journal ArticleDOI
The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing
Alvaro Martinez Barrio,Sangeet Lamichhaney,Guangyi Fan,Nima Rafati,Mats E. Pettersson,He Zhang,Jacques Dainat,Jacques Dainat,Diana Ekman,Marc P. Höppner,Marc P. Höppner,Patric Jern,Marcel Martin,Björn Nystedt,Xin Liu,Wenbin Chen,Xinming Liang,Chengcheng Shi,Yuanyuan Fu,Kailong Ma,Xiao Zhan,Chungang Feng,Ulla Gustafson,Carl-Johan Rubin,Markus Sällman Almén,Martina Blass,Michele Casini,Arild Folkvord,Linda Laikre,Nils Ryman,Simon Ming-Yuen Lee,Xun Xu,Leif Andersson,Leif Andersson,Leif Andersson +34 more
TL;DR: The results show that both coding and non-coding changes contribute to adaptation, and Haplotype blocks, often spanning multiple genes and maintained by selection, are associated with genetic differentiation.
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