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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Journal ArticleDOI
Sequence Analysis of the Mobile Genome Island pKLC102 of Pseudomonas aeruginosa C
TL;DR: The case of pKLC102 in P. aeruginosa clone C documents the intraclonal evolution of a genome island from a mobile ancestor via a reversibly integrated state to irreversible incorporation and dissipation in the chromosome.
This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. Complete genome sequence of the sugarcane nitrogen-fixing endophyte Gluconacetobacter diazotrophicus PAL5
Rodolpho Mattos Albano,Vania Lucia Muniz De Padua,Adriana Silva Hemerly,Stefan Schwab,Leonardo Franca,Viviane Magalhaes,Alexander M. Cardoso +6 more
Abstract: BackgroundGluconacetobacter diazotrophicus Pal5 is an endophytic diazotrophic bacterium that lives in association with sugarcane plants. It has important biotechnological features such as nitrogen fixation, plant growth promotion, sugar metabolism pathways, secretion of organic acids, synthesis of auxin and the occurrence of bacteriocins.ResultsGluconacetobacter diazotrophicus Pal5 is the third diazotrophic endophytic bacterium to be completely sequenced. Its genome is composed of a 3.9 Mb chromosome and 2 plasmids of 16.6 and 38.8 kb, respectively. We annotated 3,938 coding sequences which reveal several characteristics related to the endophytic lifestyle such as nitrogen fixation, plant growth promotion, sugar metabolism, transport systems, synthesis of auxin and the occurrence of bacteriocins. Genomic analysis identified a core component of 894 genes shared with phylogenetically related bacteria. Gene clusters for gum-like polysaccharide biosynthesis, tad pilus, quorum sensing, for modulation of plant growth by indole acetic acid and mechanisms involved in tolerance to acidic conditions were identified and may be related to the sugarcane endophytic and plant-growth promoting traits of G. diazotrophicus. An accessory component of at least 851 genes distributed in genome islands was identified, and was most likely acquired by horizontal gene transfer. This portion of the genome has likely contributed to adaptation to the plant habitat.ConclusionThe genome data offer an important resource of information that can be used to manipulate plant/bacterium interactions with the aim of improving sugarcane crop production and other biotechnological applications.
Journal ArticleDOI
The mitochondrial genome of the blowfly Chrysomya chloropyga (Diptera: Calliphoridae).
Ana Carolina M. Junqueira,Ana Cláudia Lessinger,Tatiana Teixeira Torres,Felipe Rodrigues da Silva,André Luiz Vettore,Paulo Arruda,Ana Maria Lima de Azeredo Espin +6 more
TL;DR: In this paper, the mitochondrial genome of the blowfly Chrysomya chloropyga (Diptera: Calliphoridae) was completely sequenced using the shotgun approach and the overall nucleotide composition was heavily biased towards As and Ts, which accounted for 76.7% of the whole genome.
Journal ArticleDOI
Genome of the human hookworm Necator americanus
Yat T. Tang,Xin Gao,Bruce A. Rosa,Sahar Abubucker,Kymberlie Hallsworth-Pepin,John Martin,Rahul Tyagi,Esley M. Heizer,Xu Zhang,Veena Bhonagiri-Palsikar,Patrick Minx,Wesley C. Warren,Qi Wang,Bin Zhan,Peter J. Hotez,Paul W. Sternberg,Paul W. Sternberg,Annette M. Dougall,Soraya Gaze,Jason Mulvenna,Javier Sotillo,Shoba Ranganathan,Shoba Ranganathan,Élida Mara Leite Rabelo,Richard K. Wilson,Philip L. Felgner,Jeffrey M. Bethony,John M. Hawdon,Robin B. Gasser,Alex Loukas,Makedonka Mitreva +30 more
TL;DR: Characterization of this first hookworm genome sequence identified genes orchestrating the hookworm's invasion of the human host, genes involved in blood feeding and development, and genes encoding proteins that represent new potential drug targets against hookworms.
Journal ArticleDOI
Complete Genome Sequence of the Dehalorespiring Bacterium Desulfitobacterium hafniense Y51 and Comparison with Dehalococcoides ethenogenes 195
Hiroshi Nonaka,Gabor Keresztes,Yoshifumi Shinoda,Yuko Ikenaga,Miyuki Abe,Kae Naito,Ken-ichi Inatomi,Kensuke Furukawa,Masayuki Inui,Hideaki Yukawa +9 more
TL;DR: A genomic comparison of the PCE-dechlorinating strain Desulfitobacterium hafniense Y51 and the Dehalococcoides ethenogenes 195 strains allowed us to narrow down the potential candidates implicated in the dechlorination process.
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COMPLETE GENOME SEQUENCE OF THE METHANOGENIC ARCHAEON, $i(METHANOCOCCUS JANNASCHII)
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