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
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Neogastropod phylogenetic relationships based on entire mitochondrial genomes.
TL;DR: Phylogenetic analyses based on complete mt genome data resolved a higher number of internal branches of the caenogastropod tree than individual mt genes, and maximum likelihood (ML) and Bayesian inference (BI) phylogenetic analyses failed to recover the monophyly of Neogastopoda due to the inclusion of the tonnoidean Cymatium parthenopeum within the group.
Journal ArticleDOI
Mitogenomic analysis of decapod crustacean phylogeny corroborates traditional views on their relationships
TL;DR: It is thought that the largely stable topology of the trees regardless of different types of analyses suggests that mitochondrial genomes show good potential to resolve the relationship within Decapoda.
Journal ArticleDOI
RAIN: RNA-protein Association and Interaction Networks.
Alexander Junge,Jan C. Refsgaard,Christian Garde,Christian Garde,Xiaoyong Pan,Alberto Santos,Ferhat Alkan,Christian Anthon,Christian von Mering,Christopher T. Workman,Christopher T. Workman,Lars Juhl Jensen,Jan Gorodkin +12 more
TL;DR: It is demonstrated that RAIN outperforms the underlying microRNA-target predictions in inferring ncRNA interactions and its integration with the STRING database of protein–protein interactions.
Journal ArticleDOI
How mutations in tRNA distant from the anticodon affect the fidelity of decoding
TL;DR: In this paper, the authors present crystal structures of the 70S ribosome complex with EF-Tu and aminoacyl tRNA (native tRNA(Trp), G24A tRNAs, or the miscoding A9C tRNMs) bound to cognate UGG or near-cognate UGA codons, determined at 3.2-A resolution.
Journal ArticleDOI
Population genomics shows no distinction between pathogenic Candida krusei and environmental Pichia kudriavzevii : One species, four names
Alexander P Douglass,Benjamin Offei,Stephanie Braun-Galleani,Aisling Y. Coughlan,Alexandre A. R. Martos,Raúl A. Ortiz-Merino,Kevin P. Byrne,Kenneth H. Wolfe +7 more
TL;DR: In this article, the authors investigated the genomic diversity of a yeast species that is both an opportunistic pathogen and an important industrial yeast, which is responsible for about 2% of yeast infections caused by Candida species in humans.
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