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
The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution.
Daniel Lang,Kristian K. Ullrich,Florent Murat,Joerg Fuchs,Jerry Jenkins,Fabian B. Haas,Mathieu Piednoël,Heidrun Gundlach,Michiel Van Bel,Rabea Meyberg,Cristina Vives,Jordi Morata,Aikaterini Symeonidi,Manuel Hiss,Wellington Muchero,Yasuko Kamisugi,Omar Abu Saleh,Guillaume Blanc,Eva L. Decker,Nico van Gessel,Jane Grimwood,Richard D. Hayes,Sean W. Graham,Lee E. Gunter,Stuart F. McDaniel,Sebastian N. W. Hoernstein,Anders Larsson,Fay-Wei Li,Pierre-François Perroud,Jeremy Phillips,Priya Ranjan,Daniel S. Rokshar,Daniel S. Rokshar,Carl J. Rothfels,Lucas Schneider,Shengqiang Shu,Dennis W. Stevenson,Fritz Thümmler,Michael Tillich,Juan Carlos Villarreal Aguilar,Thomas Widiez,Thomas Widiez,Gane Ka-Shu Wong,Ann M. Wymore,Yong Zhang,Andreas Zimmer,Ralph S. Quatrano,Klaus F. X. Mayer,David Goodstein,Josep M. Casacuberta,Klaas Vandepoele,Ralf Reski,Andrew C. Cuming,Gerald A. Tuskan,Florian Maumus,Jérôme Salse,Jeremy Schmutz,Stefan A. Rensing,Stefan A. Rensing +58 more
TL;DR: More non-seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes, it is found that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle.
Journal ArticleDOI
The draft genome of the parasitic nematode Trichinella spiralis
Makedonka Mitreva,Douglas P. Jasmer,Dante S. Zarlenga,Zhengyuan Wang,Sahar Abubucker,John Martin,Christina M. Taylor,Yong Yin,Yong Yin,Lucinda Fulton,Patrick Minx,Shiaw-Pyng Yang,Shiaw-Pyng Yang,Wesley C. Warren,Robert S. Fulton,Veena Bhonagiri,Xu Zhang,Kym Hallsworth-Pepin,Sandra W. Clifton,James P. McCarter,Judith A. Appleton,Elaine R. Mardis,Richard K. Wilson +22 more
TL;DR: A draft genome sequence of Trichinella spiralis, a food-borne zoonotic parasite, which is the most common cause of human trichinellosis is reported, enabling identification of archetypical genes and molecular signatures exclusive to nematodes.
Posted ContentDOI
tRNAscan-SE 2.0: Improved Detection and Functional Classification of Transfer RNA Genes
TL;DR: Overall, tRNA detection sensitivity and specificity is improved for all isotypes, particularly those utilizing specialized models for selenocysteine and the three subtypes of tRNA genes encoding a CAU anticodon.
Journal ArticleDOI
Complete genome structure of Gloeobacter violaceus PCC 7421, a cyanobacterium that lacks thylakoids.
Yasukazu Nakamura,Takakazu Kaneko,Shusei Sato,Mamoru Mimuro,Hideaki Miyashita,Tohru Tsuchiya,Shigemi Sasamoto,Akiko Watanabe,Kumiko Kawashima,Yoshie Kishida,Chiaki Kiyokawa,Mitsuyo Kohara,Midori Matsumoto,Ai Matsuno,Naomi Nakazaki,Sayaka Shimpo,Chie Takeuchi,Manabu Yamada,Satoshi Tabata +18 more
TL;DR: A large number of genes for sigma factors and transcription factors in the LuxR, LysR, PadR, TetR, and MarR families could be identified, while those for major elements for circadian clock, kaiABC were not found, which may reflect the phylogenetic distance between G. violaceus and other cyanobacteria.
The NCBI Handbook
Jo McEntyre,Jim Ostell +1 more
TL;DR: Maintaining all data in the same structured format simplifies data parsing, manipulation, and quality assurance, and eases the task of data integration and software development for sequence analysis.
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