SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data.
TLDR
SortMeRNA, a new software designed to rapidly filter rRNA fragments from metatranscriptomic data, is presented, capable of handling large sets of reads and sorting out all fragments matching to the rRNA database with high sensitivity and low running time.Abstract:
MOTIVATION: The application of Next-Generation Sequencing (NGS) technologies to RNAs directly extracted from a community of organisms yields a mixture of fragments characterizing both coding and non-coding types of RNAs. The tasks to distinguish among these and to further categorize the families of messenger RNAs and ribosomal RNAs is an important step for examining gene expression patterns of an interactive environment and the phylogenetic classification of the constituting species. RESULTS: We present SortMeRNA, a new software designed to rapidly filter ribosomal RNA fragments from metatranscriptomic data. It is capable of handling large sets of reads and sorting out all fragments matching to the rRNA database with high sensitivity and low running time. AVAILABILITY: http://bioinfo.lifl.fr/RNA/sortmerna CONTACT: evguenia.kopylova@lifl.fr SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.read more
Citations
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Low abundance of methanotrophs in sediments of shallow boreal coastal zones with high water methane concentrations
Elias Broman,Xiaole Sun,Christian Stranne,Marco G. Salgado,Stefano Bonaglia,Stefano Bonaglia,Marc C. Geibel,Martin Jakobsson,Alf Norkko,Christoph Humborg,Christoph Humborg,Francisco J. A. Nascimento +11 more
TL;DR: The relative abundance and RNA transcripts attributed to the CH4 oxidizing protein (pMMO; particulate methane monooxygenase) of the dominant methanotroph Methylococcales was significantly higher in deeper costal offshore areas (36–45 m water depth) compared to adjacent shallow zones, which can partly explain the difference in CH4 concentrations between shallow and deep coastal areas, and the relationship betweenCH4 concentrations and water depth.
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Metatranscriptomic insight into the effects of antibiotic exposure on performance during anaerobic co-digestion of food waste and sludge
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Asymmetric distribution of biomolecules of maternal origin in the Xenopus laevis egg and their impact on the developmental plan.
Radek Sindelka,Pavel Abaffy,Yanyan Qu,Silvie Tománková,Monika Sidova,Ravindra Naraine,Michal Kolar,Elizabeth H. Peuchen,Liangliang Sun,Liangliang Sun,Norman J. Dovichi,Mikael Kubista +11 more
TL;DR: Subcellular transcriptomic and proteomic analyses along the animal-vegetal axis of Xenopus laevis eggs and a possible mechanism of genetic evolution are presented, based on unexpected observation of the profiles of the homoeologous genes exd2.
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Red Sea SAR11 and Prochlorococcus Single-Cell Genomes Reflect Globally Distributed Pangenomes.
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TL;DR: The Red Sea is isolated geographically from the rest of the ocean and has a combination of high irradiance, high temperature, and high salinity that is unique among the oceans; it is asked whether it harbors endemic gene content, and results suggest that Baas Becking's hypothesis “everything is everywhere, but the environment selects” also applies to gene ortholog groups.
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Hybrid de novo transcriptome assembly of poinsettia (Euphorbia pulcherrima Willd. Ex Klotsch) bracts.
Vinicius Vilperte,Calin Rares Lucaciu,Heidi Halbwirth,Robert Boehm,Thomas Rattei,Thomas Debener +5 more
TL;DR: A transcriptome analysis of red- and white-bracted poinsettia varieties showed a differential regulation of the flavonoid biosynthesis pathway only at particular stages of bract development, and GSTF11 and UGT79B10 showed a lower expression in the last stage of bracted development for the white variety and, therefore, are potential candidates for further studies on poinsetti coloration.
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