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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The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut.
Ann C. Gregory,Olivier Zablocki,Ahmed A. Zayed,Allison Howell,Benjamin Bolduc,Matthew B. Sullivan +5 more
TL;DR: The GVD meta-analyses show highly personalized viromes, reveal that inter-study variability from technical artifacts is larger than any “disease” effect at the population level, and document how viral diversity changes from human infancy into senescence.
Journal ArticleDOI
The Genome Sequence of Mycoplasma hyopneumoniae Strain 232, the Agent of Swine Mycoplasmosis
F. Chris Minion,Elliot J. Lefkowitz,Melissa L. Madsen,Barbara J. Cleary,Steven Swartzell,Gregory G. Mahairas +5 more
TL;DR: The complete genome sequence of Mycoplasma hyopneumoniae, an important member of the porcine respiratory disease complex, is presented, finding few genes with tandem repeat sequences that could be involved in phase switching or antigenic variation and it is not clear how M. hyop pneumoniae evades the immune response and establishes a chronic infection.
Journal ArticleDOI
Genome Sequence of an M3 Strain of Streptococcus pyogenes Reveals a Large-Scale Genomic Rearrangement in Invasive Strains and New Insights into Phage Evolution
Ichiro Nakagawa,Ken Kurokawa,Atsushi Yamashita,Masanobu Nakata,Yusuke Tomiyasu,Nobuo Okahashi,Shigetada Kawabata,Kiyoshi Yamazaki,Tadayoshi Shiba,Teruo Yasunaga,Hideo Hayashi,Masahira Hattori,Shigeyuki Hamada +12 more
TL;DR: Observations indicate that streptococcal phages represent important plasticity regions in the GAS chromosome where recombination between homologous phage genes can occur and result not only in new phage derivatives, but also in large chromosomal rearrangements.
Journal ArticleDOI
The complete nucleotide sequence and multipartite organization of the tobacco mitochondrial genome: comparative analysis of mitochondrial genomes in higher plants.
TL;DR: The complete mtDNA sequence of Nicotiana tabacum is determined and it is revealed that there are four classes of boundaries derived from homologous recombination, which leads to a multipartite organization with two MCs and six subgenomic circles.
The comprehensive microbial resource
Tanja Davidsen,Erin Beck,Anuradha Ganapathy,Robert R. Montgomery,Nikhat Zafar,Qi Yang,Ramana Madupu,Phil Goetz,Kevin Galinsky,Owen White,Granger G. Sutton +10 more
TL;DR: The Comprehensive Microbial Resource or CMR provides a web-based central resource for the display, search and analysis of the sequence and annotation for complete and publicly available bacterial and archaeal genomes.
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COMPLETE GENOME SEQUENCE OF THE METHANOGENIC ARCHAEON, $i(METHANOCOCCUS JANNASCHII)
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