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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De novo transcriptome assembly of mangosteen (Garcinia mangostana L.) fruit.
TL;DR: De novo transcriptomic analysis of Garcinia mangostana L. (Mangosteen) through RNA-Seq technology is performed and it is shown that transcriptomic data obtained will be beneficial for studying transcriptome of the fruit.
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Comparative transcriptome analysis of two contrasting resistant and susceptible Aegilops tauschii accessions to wheat leaf rust (Puccinia triticina) using RNA-sequencing
TL;DR: In this paper , a comparative transcriptome analysis of Aegilops-P. triticina interaction was performed using RNA-sequencing to reveal the strength and weakness of wheat resistance to leaf rust and exhibits a pipeline for future wheat breeding programs.
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Getting to Know the Gut Microbial Diversity of Metropolitan Buenos Aires Inhabitants.
Fiorella Sabrina Belforte,Fiorella Sabrina Belforte,Natalie Fernandez,Francisco Tonín Monzón,Ayelén Daiana Rosso,Sofía Quesada,María Cecilia Cimolai,María Cecilia Cimolai,Andrea Millán,Gloria Edith Cerrone,Gustavo Daniel Frechtel,Rémy Burcelin,Rémy Burcelin,Federico Coluccio Leskow,Federico Coluccio Leskow,Alberto Penas-Steinhardt +15 more
TL;DR: The uncharacterized metagenome of the Buenos Aires (BA) city population and its metropolitan area, being the second most populated agglomeration in the southern hemisphere, is evaluated to promote research and comparison of the microbiome in different human populations, in order to develop more efficient therapeutic strategies for the restoration of a healthy dialogue between host and environment.
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Low temperature upregulates cwp expression and modifies alternative splicing patterns, increasing the severity of cwp-induced tomato fruit cuticular microfissures.
Noam Chechanovsky,Ran Hovav,Rina Frenkel,Adi Faigenboim,Yelena Eselson,Marina Petreikov,Michal Moy,Shmuel Shen,Arthur A. Schaffer +8 more
TL;DR: The molecular mechanism behind the horticultural phenomenon of the low-temperature effect on cuticular microfissures in the dehydrating tomato is demonstrated.
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Role of Dicer-Dependent RNA Interference in Regulating Mycoparasitic Interactions.
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TL;DR: In this article, the role of DCL-dependent RNA interference in mycoparasitic interactions between C. rosea and B. cinerea and Fusarium graminearum was investigated.
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