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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Comparative Analysis of Gender-Associated Complete Mitochondrial Genomes in Marine Mussels (Mytilus spp.)
TL;DR: Correlation of the divergence rate of different protein-coding genes indicates that mtDNA-encoded proteins of the M genome are still under selective constraints, although less highly than genes of the F genome.
Journal ArticleDOI
Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines
Charlotte D. Vavourakis,Rohit Ghai,Francisco Rodriguez-Valera,Dimitry Y. Sorokin,Susannah G. Tringe,Philip Hugenholtz,Gerard Muyzer +6 more
TL;DR: The first “metagenomic snapshots” of microbial communities thriving in the brines of four shallow soda lakes from the Kulunda Steppe (Altai, Russia) covering a salinity range from 170 to 400 g/L are presented.
Journal ArticleDOI
Potential Retroviruses in Plants: Tat1 Is Related to a Group of Arabidopsis thaliana Ty3/gypsy Retrotransposons That Encode Envelope-Like Proteins
David A. Wright,Daniel F. Voytas +1 more
TL;DR: Evidence is provided that Tat1 is a retrotransposon and that previously described insertions are solo long terminal repeats left behind after the deletion of coding regions of full-length elements, which suggests that Tat/Athila Retrotransposons may produce enveloped virions and may be infectious.
Journal ArticleDOI
The genome of tolypocladium inflatum: evolution, organization, and expression of the cyclosporin biosynthetic gene cluster.
Kathryn E. Bushley,Rajani Raja,Pankaj Jaiswal,Jason S. Cumbie,Mariko Nonogaki,Alexander Boyd,C. Alisha Owensby,Brian J. Knaus,Justin Elser,Daniel Miller,Yanming Di,Kerry L. McPhail,Joseph W. Spatafora +12 more
TL;DR: The T. inflatum genome provides additional insight into the evolution and biosynthesis of cyclosporin and lays a foundation for further investigations of the role of secondary metabolite gene clusters and their metabolites in fungal biology.
Journal ArticleDOI
A mitochondrial genome phylogeny of termites (Blattodea Termitoidae): Robust support for interfamilial relationships and molecular synapomorphies define major clades
TL;DR: A highly supported tree of termite relationships was produced, however the relationship of the termites+Cryptocercus clade to other cockroach lineages was highly affected by the strong nucleotide compositional bias found in termites relative to other dictyopterans.
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