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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Reductive Evolution of Bacterial Genome in Insect Gut Environment
TL;DR: The complete genome sequence of such a gut bacterium Ishikawaella capsulata of the plataspid stinkbug Megacopta punctatissima is reported, highlighting strikingly similar evolutionary patterns that are shared between the extracellular and endocellular insect symbiont genomes.
Journal ArticleDOI
Bacterial Biosynthesis and Maturation of the Didemnin Anti-cancer Agents
Ying Xu,Roland D. Kersten,Sang Jip Nam,Liang Lu,Abdulaziz M. Al-Suwailem,Huajun Zheng,William Fenical,Pieter C. Dorrestein,Bradley S. Moore,Bradley S. Moore,Pei-Yuan Qian +10 more
TL;DR: It is shown that the didemnins are bacterial products produced by the marine α-proteobacteria Tistrella mobilis and Tistrell bauzanensis via a unique post-assembly line maturation process and may provide a long-term solution to the supply problem that presently hinders this group of marine natural products.
Journal ArticleDOI
Metazoan tRNA introns generate stable circular RNAs in vivo.
Zhipeng Lu,Grigory S. Filonov,John J. Noto,Casey A. Schmidt,Talia Hatkevich,Ying Wen,Samie R. Jaffrey,A. Gregory Matera +7 more
TL;DR: A class of abundant circular noncoding RNAs that are produced during metazoan tRNA splicing are discovered and an in vivo expression system for generating "designer" circular RNAs in human cells is developed.
Journal ArticleDOI
Folding and Finding RNA Secondary Structure
TL;DR: Methods are reviewed that automate folding and discovery of RNAs with algorithms that couple thermodynamics with chemical mapping, NMR, and/or sequence comparison to provide insights into evolution, biology, and design of therapeutics.
Journal ArticleDOI
The complete mitochondrial genomes of two ghost moths, Thitarodes renzhiensis and Thitarodes yunnanensis: the ancestral gene arrangement in Lepidoptera.
TL;DR: Characterization of the two ghost moth mitogenomes has enriched the knowledge of Lepidoptera mitagenomes and contributed to the understanding of the mechanisms underlying mitogenome evolution, especially gene rearrangements.
References
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