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 genome of the recently domesticated crop plant sugar beet ( Beta vulgaris )
Juliane C. Dohm,André E. Minoche,Daniela Holtgräwe,Salvador Capella-Gutierrez,Falk Zakrzewski,Hakim Tafer,Oliver Rupp,Thomas Rosleff Sörensen,Ralf Stracke,Richard Reinhardt,Alexander Goesmann,Thomas Kraft,Britta Schulz,Peter F. Stadler,Thomas Schmidt,Toni Gabaldón,Hans Lehrach,Bernd Weisshaar,Heinz Himmelbauer +18 more
TL;DR: A reference genome sequence for sugar beet is presented as the first non-rosid, non-asterid eudicot genome, advancing comparative genomics and phylogenetic reconstructions and provides evidence for the separation of Caryophyllales before the split of asterids and rosids, and revealed lineage-specific gene family expansions and losses.
Journal ArticleDOI
A unified catalog of 204,938 reference genomes from the human gut microbiome.
Alexandre Almeida,Alexandre Almeida,Stephen Nayfach,Stephen Nayfach,Miguel Boland,Francesco Strozzi,Martin Beracochea,Zhou Jason Shi,Katherine S. Pollard,Ekaterina A. Sakharova,Donovan H. Parks,Philip Hugenholtz,Nicola Segata,Nikos C. Kyrpides,Nikos C. Kyrpides,Robert D. Finn +15 more
TL;DR: The Unified Human Gastrointestinal Genome (UHGG) collection, comprising 204,938 nonredundant genomes from 4,644 gut prokaryotes, is presented, providing comprehensive resources for microbiome researchers.
Journal ArticleDOI
Chromosome 2 Sequence of the Human Malaria Parasite Plasmodium falciparum
Malcolm J. Gardner,Herve Tettelin,Daniel J. Carucci,Leda M. Cummings,L. Aravind,Eugene V. Koonin,Shamira J. Shallom,Tanya Mason,Kelly Yu,Claire Fujii,James Pederson,Kun Shen,Junping Jing,Christopher Aston,Zhongwu Lai,David C. Schwartz,Mihaela Pertea,Steven L. Salzberg,Lixin Zhou,Granger G. Sutton,Rebecca A. Clayton,Owen White,Hamilton O. Smith,Claire M. Fraser,Mark D. Adams,J. Craig Venter,Stephen L. Hoffman +26 more
TL;DR: Chromosome 2 of Plasmodium falciparum was sequenced; this sequence contains 947,103 base pairs and encodes 210 predicted genes as discussed by the authors.
Journal ArticleDOI
Draft genome sequence of the oilseed species Ricinus communis
Agnes P. Chan,Jonathan Crabtree,Qi Zhao,Hernan Lorenzi,Joshua Orvis,Daniela Puiu,Admasu Melake-Berhan,Kristine M Jones,Julia C. Redman,Grace Q. Chen,Edgar B. Cahoon,Melaku Gedil,Mario Stanke,Brian J. Haas,Jennifer R. Wortman,Claire M. Fraser-Liggett,Jacques Ravel,Pablo D. Rabinowicz,Pablo D. Rabinowicz +18 more
TL;DR: Comparative genomics analysis suggests the presence of an ancient hexaploidization event that is conserved across the dicotyledonous lineage and the number of members of the ricin gene family is larger than previously thought.
Journal ArticleDOI
Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes
Daniel E. Neafsey,Robert M. Waterhouse,Mohammad Reza Abai,Sergey Aganezov,Max A. Alekseyev,James E. Allen,James Amon,Bruno Arcà,Peter Arensburger,Gleb N. Artemov,Lauren A. Assour,Hamidreza Basseri,Aaron M. Berlin,Bruce W. Birren,Stéphanie Blandin,Stéphanie Blandin,Andrew I. Brockman,Thomas R. Burkot,Austin Burt,Clara S. Chan,Cedric Chauve,Joanna C. Chiu,Mikkel B. Christensen,Carlo Costantini,Victoria L.M. Davidson,Elena Deligianni,Tania Dottorini,Vicky Dritsou,Stacey Gabriel,Wamdaogo M. Guelbeogo,Andrew Brantley Hall,Mira V. Han,Thaung Hlaing,Daniel S.T. Hughes,Daniel S.T. Hughes,Adam M. Jenkins,Xiaofang Jiang,Irwin Jungreis,Evdoxia G. Kakani,Evdoxia G. Kakani,Maryam Kamali,Petri Kemppainen,Ryan C. Kennedy,Ioannis K. Kirmitzoglou,Ioannis K. Kirmitzoglou,Lizette L. Koekemoer,Njoroge Laban,Nicholas Langridge,Mara K. N. Lawniczak,Manolis Lirakis,Neil F. Lobo,Ernesto Lowy,Robert M. MacCallum,Chunhong Mao,Gareth Maslen,Charles Mbogo,Jenny McCarthy,Kristin Michel,Sara N. Mitchell,Wendy Moore,Katherine A. Murphy,Anastasia N. Naumenko,Tony Nolan,Eva Maria Novoa,Samantha M. O’Loughlin,Chioma Oringanje,Mohammad Ali Oshaghi,Nazzy Pakpour,Philippos Aris Papathanos,Philippos Aris Papathanos,Ashley Peery,Michael Povelones,Anil Prakash,David P. Price,Ashok Rajaraman,Lisa J. Reimer,David C. Rinker,Antonis Rokas,Tanya L. Russell,N’Fale Sagnon,Maria V. Sharakhova,Terrance Shea,Felipe A. Simão,Felipe A. Simão,Frédéric Simard,Michel A. Slotman,Pradya Somboon,V. N. Stegniy,Claudio J. Struchiner,Claudio J. Struchiner,Gregg W.C. Thomas,Marta Tojo,Pantelis Topalis,Jose M. C. Tubio,Maria F. Unger,John Vontas,Catherine Walton,Craig S. Wilding,Judith H. Willis,Yi-Chieh Wu,Yi-Chieh Wu,Guiyun Yan,Evgeny M. Zdobnov,Evgeny M. Zdobnov,Xiaofan Zhou,Flaminia Catteruccia,Flaminia Catteruccia,George K. Christophides,Frank H. Collins,Robert S. Cornman,Andrea Crisanti,Andrea Crisanti,Martin J. Donnelly,Martin J. Donnelly,Scott J. Emrich,Michael C. Fontaine,Michael C. Fontaine,William M. Gelbart,Matthew W. Hahn,Immo A. Hansen,Paul I. Howell,Fotis C. Kafatos,Manolis Kellis,Daniel Lawson,Christos Louis,Shirley Luckhart,Marc A. T. Muskavitch,Marc A. T. Muskavitch,José M. C. Ribeiro,Michael A. Riehle,Igor V. Sharakhov,Zhijian Tu,Laurence J. Zwiebel,Nora J. Besansky +133 more
TL;DR: The authors investigated the genomic basis of vectorial capacity and explore new avenues for vector control, sequenced the genomes of 16 anopheline mosquito species from diverse locations spanning ~100 million years of evolution Comparative analyses show faster rates of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses, relative to Drosophila.
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