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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GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses
John Besemer,Mark Borodovsky +1 more
TL;DR: The task of gene identification frequently confronting researchers working with both novel and well studied genomes can be conveniently and reliably solved with the help of the GeneMark web software.
Journal ArticleDOI
An evolutionarily conserved mechanism for controlling the efficiency of protein translation.
Tamir Tuller,Asaf Carmi,Kalin Vestsigian,Sivan Navon,Yuval Dorfan,John M. Zaborske,Tao Pan,Orna Dahan,Itay Furman,Yitzhak Pilpel +9 more
TL;DR: It is suggested that the slow "ramp" at the beginning of mRNAs serves as a late stage of translation initiation, forming an optimal and robust means to reduce ribosomal traffic jams, thus minimizing the cost of protein expression.
Journal ArticleDOI
Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti.
Takakazu Kaneko,Yasukazu Nakamura,Shusei Sato,Erika Asamizu,Tomohiko Kato,Shigemi Sasamoto,Akiko Watanabe,Kumi Idesawa,Atsuko Ishikawa,Kumiko Kawashima,Takaharu Kimura,Yoshie Kishida,Chiaki Kiyokawa,Mitsuyo Kohara,Midori Matsumoto,Ai Matsuno,Yoko Mochizuki,Shinobu Nakayama,Naomi Nakazaki,Sayaka Shimpo,Masako Sugimoto,Chie Takeuchi,Manabu Yamada,Satoshi Tabata +23 more
TL;DR: The complete nucleotide sequence of the genome of a symbiotic bacterium Mesorhizobium loti strain MAFF303099 was determined and suggested that the symbiotic island as well as the plasmids originated and were transmitted from other genetic systems.
Journal ArticleDOI
Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110.
Takakazu Kaneko,Yasukazu Nakamura,Shusei Sato,Kiwamu Minamisawa,Toshiki Uchiumi,Shigemi Sasamoto,Akiko Watanabe,Kumi Idesawa,Mayumi Iriguchi,Kumiko Kawashima,Mitsuyo Kohara,Midori Matsumoto,Sayaka Shimpo,Hisae Tsuruoka,Tsuyuko Wada,Manabu Yamada,Satoshi Tabata +16 more
TL;DR: Observations suggest plasticity of the B. japonicum genome is probably due to complex genome rearrangements such as horizontal transfer and insertion of various DNA elements, and to homologous recombination.
References
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COMPLETE GENOME SEQUENCE OF THE METHANOGENIC ARCHAEON, $i(METHANOCOCCUS JANNASCHII)
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