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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Exploring patterns and extent of bias in estimating divergence time from mitochondrial DNA sequence data in a particular lineage: A case study of salamanders (Order Caudata)
TL;DR: Assessment of the effects of saturation on dating divergences using mitochondrial genome sequences on a timescale of ~200-300 My indicated that dates derived from the mitochondrial data were considerably overestimated and systematically biased toward the calibration point for the ingroup root.
Journal ArticleDOI
Comparative genomics of mutualistic viruses of Glyptapanteles parasitic wasps.
Christopher A. Desjardins,Christopher A. Desjardins,Dawn E. Gundersen-Rindal,Jessica B. Hostetler,Luke J. Tallon,Luke J. Tallon,Douglas Fadrosh,Roger W. Fuester,Monica J. Pedroni,Monica J. Pedroni,Brian J. Haas,Brian J. Haas,Michael C. Schatz,Kristine M Jones,Kristine M Jones,Jonathan Crabtree,Jonathan Crabtree,Heather Forberger,Vishvanath Nene,Vishvanath Nene +19 more
TL;DR: Phylogenetic analyses of the bracoviral genes encoding sugar transporters provides the first robust evidence of a wasp origin for some polydnavirus genes, and it is hypothesized transposable elements, such as those described here, could facilitate transfer of genes between proviral segments and host DNA.
Journal ArticleDOI
Frequent mitochondrial gene rearrangements at the hymenopteran nad3-nad5 junction.
TL;DR: The organization of mitochondrial genes from a diverse range of hymenopterans was characterized, and local inversions were relatively common, i.e., rearrangements characterized by the movement of genes from one mitochondrial strand to the other, opposite or close to their ancestral position.
Journal ArticleDOI
HAMR: high-throughput annotation of modified ribonucleotides
Paul Ryvkin,Yuk Yee Leung,Ian M. Silverman,Micah Childress,Otto Valladares,Isabelle Dragomir,Brian D. Gregory,Li-San Wang +7 more
TL;DR: A method that can not only locate these modifications transcriptome-wide with single nucleotide resolution, but can also differentiate between different classes of modifications is developed, finding that different modifications produce distinct patterns of cDNA sequence.
Journal ArticleDOI
Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels.
Milana Frenkel-Morgenstern,Tamar Danon,Thomas Christian,Takao Igarashi,Lydia Cohen,Ya-Ming Hou,Lars Juhl Jensen +6 more
TL;DR: The data indicate that cells exploit wobbling to generate cell cycle‐dependent dynamics of proteins, and it is proposed that non‐optimal (wobbly) matching codons influence protein synthesis during the cell cycle.
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COMPLETE GENOME SEQUENCE OF THE METHANOGENIC ARCHAEON, $i(METHANOCOCCUS JANNASCHII)
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