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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Complete chloroplast genome of the multifunctional crop globe artichoke and comparison with other Asteraceae.
Pasquale Luca Curci,Domenico De Paola,Donatella Danzi,Giovanni G. Vendramin,Gabriella Sonnante +4 more
TL;DR: The results highlight the usefulness of cp genome sequencing in exploring plant genome diversity and retrieving reliable molecular resources for phylogenetic and evolutionary studies, as well as for specific barcodes in plants.
Journal ArticleDOI
A mobile pathogenicity chromosome in Fusarium oxysporum for infection of multiple cucurbit species
Peter van Dam,Like Fokkens,Yu Ayukawa,Michelle van der Gragt,Anneliek M. ter Horst,Balázs Brankovics,Petra M. Houterman,Tsutomu Arie,Martijn Rep +8 more
TL;DR: It is concluded that also a non-wilt-inducing Fo pathogen relies on effector proteins for successful infection and that the Forc pathogenicity chromosome contains all the information necessary for causing root rot of cucurbits.
Journal ArticleDOI
Long tail fibres of the novel broad‐host‐range T‐even bacteriophage S16 specifically recognize Salmonella OmpC
TL;DR: Its virulent nature, broad host range and apparent lack of host DNA transduction render S16 highly suitable for biocontrol of Salmonella in foods and animal production.
Journal ArticleDOI
Pegasys: software for executing and integrating analyses of biological sequences.
Sohrab P. Shah,David Y. M. He,J. Sawkins,Jeffrey C. Druce,Gerald Quon,Drew Lett,Grace X.Y. Zheng,Tao Xu,B. F. Francis Ouellette +8 more
TL;DR: A novel data structure is introduced for creating workflows of sequence analyses and a unified data model to store its results in the Pegasys system, which enables biologists and bioinformaticians to create and manage sequence analysis workflows.
Journal ArticleDOI
Comparative genomics reveals a deep-sea sediment-adapted life style of Pseudoalteromonas sp. SM9913
Qi-Long Qin,Yang Li,Yan-Jiao Zhang,Zhemin Zhou,Wei-Xin Zhang,Xiu-Lan Chen,Xi-Ying Zhang,Bai-Cheng Zhou,Lei Wang,Yu-Zhong Zhang +9 more
TL;DR: The complete genome of deep-sea sedimentary bacterium SM9913 is described and compared with that of the closely related Antarctic surface sea-water ecotype Pseudoalteromonas haloplanktis TAC125, indicating a possible sensitivity to reactive oxygen species.
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