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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Sex hormone-dependent tRNA halves enhance cell proliferation in breast and prostate cancers
Shozo Honda,Phillipe Loher,Megumi Shigematsu,Juan P. Palazzo,Ryusuke Suzuki,Issei Imoto,Isidore Rigoutsos,Yohei Kirino +7 more
TL;DR: A novel type of transfer RNA (tRNA)-derived small RNA, termed Sex HOrmone-dependent TRNA-derived RNAs (SHOT-RNAs), are specifically and abundantly expressed in estrogen receptor (ER)-positive breast cancer and androgen receptor (AR)-positive prostate cancer cell lines.
Journal ArticleDOI
Complete genome sequencing of Anaplasma marginale reveals that the surface is skewed to two superfamilies of outer membrane proteins
Kelly A. Brayton,Lowell S. Kappmeyer,David R. Herndon,Michael J. Dark,David L. Tibbals,Guy H. Palmer,Travis C. McGuire,Donald P. Knowles +7 more
TL;DR: By sequencing and annotating the complete 1,197,687-bp genome of the St. Maries strain of A. marginale, it is shown that this surface coat is dominated by two families containing immunodominant proteins: the msp2 superfamily and the mSP1 superfamily.
Journal ArticleDOI
Megabase Level Sequencing Reveals Contrasted Organization and Evolution Patterns of the Wheat Gene and Transposable Element Spaces
Frédéric Choulet,Thomas Wicker,Camille Rustenholz,Etienne Paux,Jérôme Salse,Philippe Leroy,Stéphane Schlub,Marie-Christine Le Paslier,Ghislaine Magdelenat,Catherine Gonthier,Arnaud Couloux,Hikmet Budak,James Breen,Michael O. Pumphrey,Sixin Liu,Xiuying Kong,Jizeng Jia,Marta Gut,Dominique Brunel,James A. Anderson,Bikram S. Gill,Rudi Appels,Beat Keller,Catherine Feuillet +23 more
TL;DR: The molecular analysis of large contiguous sequences produced from the bread wheat genome provides novel insights into the number, distribution, and density of genes along chromosome 3B and reveals an unexpectedly high amount of noncollinear genes compared to model grass genomes.
Journal ArticleDOI
Draft Genome of the Pearl Oyster Pinctada fucata: A Platform for Understanding Bivalve Biology
Takeshi Takeuchi,Takeshi Kawashima,Ryo Koyanagi,Fuki Gyoja,Makiko Tanaka,Tetsuro Ikuta,Eiichi Shoguchi,Mayuki Fujiwara,Chuya Shinzato,Kanako Hisata,Manabu Fujie,Takeshi Usami,Kiyohito Nagai,Kaoru Maeyama,Kikuhiko Okamoto,Hideo Aoki,Takashi Ishikawa,Tetsuji Masaoka,Atushi Fujiwara,Kazuyoshi Endo,Hirotoshi Endo,Hiromichi Nagasawa,Shigeharu Kinoshita,Shuichi Asakawa,Shugo Watabe,Nori Satoh +25 more
TL;DR: The draft genome of the pearl oyster provides a platform for the identification of selection markers and genes for calcification, knowledge of which will be important in the pearl industry.
Journal ArticleDOI
The genome of the square archaeon Haloquadratum walsbyi : life at the limits of water activity
Henk Bolhuis,Peter Palm,Andy Wende,Michaela Falb,Markus Rampp,Francisco Rodriguez-Valera,Friedhelm Pfeiffer,Dieter Oesterhelt +7 more
TL;DR: Although no direct genetic indication was found that can explain how this peculiar organism retains its square shape, the genome revealed several unique adaptive traits that allow this organism to thrive in its specific and extreme niche.
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