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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Giant virus with a remarkable complement of genes infects marine zooplankton.
TL;DR: Phylogenetic analysis indicates that CroV is a nucleocytoplasmic large DNA virus, with Acanthamoeba polyphaga mimivirus as its closest relative, although less than one-third of the genes of CroV have homologs in Mimivirus.
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The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus
Devin R. Scannell,Oliver A. Zill,Antonis Rokas,Celia Payen,Maitreya J. Dunham,Michael B. Eisen,Michael B. Eisen,Jasper Rine,Mark Johnston,Mark Johnston,Chris Todd Hittinger,Chris Todd Hittinger +11 more
TL;DR: Improved genome sequences of three species of Saccharomyces sensu stricto yeasts are presented, enabling a re-examination of the tempo and mode of yeast gene evolution and improved inferences of species-specific gains and losses, and genetically marked, stable haploid strains are generated for all three species.
Journal ArticleDOI
Nitrogen fixation island and rhizosphere competence traits in the genome of root-associated Pseudomonas stutzeri A1501
Yongliang Yan,Jian Yang,Yuetan Dou,Ming Chen,Shuzhen Ping,Junping Peng,Wei Lu,Wei Zhang,Ziying Yao,Hongquan Li,Wei Liu,Sheng He,Lizhao Geng,Xiaobing Zhang,Fan Yang,Haiying Yu,Yuhua Zhan,Danhua Li,Zhanglin Lin,Yi-Ping Wang,Claudine Elmerich,Min Lin,Qi Jin +22 more
TL;DR: The genome sequence offers the genetic basis for further study of the evolution of the nitrogen fixation property and identification of rhizosphere competence traits required in the interaction with host plants; moreover, it opens up new perspectives for wider application of root-associated diazotrophs in sustainable agriculture.
Journal ArticleDOI
Non Mycobacterial Virulence Genes in the Genome of the Emerging Pathogen Mycobacterium abscessus
Fabienne Ripoll,Sophie Pasek,Chantal Schenowitz,Carole Dossat,Valérie Barbe,Martin Rottman,Edouard Macheras,Beate Heym,Jean-Louis Herrmann,Mamadou Daffé,Roland Brosch,Jean-Loup Risler,Jean-Louis Gaillard +12 more
TL;DR: This study elucidates the genetic basis of the unique pathogenicity of M. abscessus among RGM, and raises the question of similar mechanisms of pathogenicicity shared by unrelated organisms in CF patients.
Journal ArticleDOI
Pyrrolysyl-tRNA synthetase: an ordinary enzyme but an outstanding genetic code expansion tool.
TL;DR: These unique but ordinary features of PylRS as an aminoacyl-tRNA synthetase allow the Pyl incorporation machinery to be easily engineered for the genetic incorporation of more than 100 non-canonical amino acids (NCAAs) or α-hydroxy acids into proteins at amber codon and the reassignment of other codons to code NCAAs.
References
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