SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data.

doi:10.1093/BIOINFORMATICS/BTS611

Open AccessJournal ArticleDOI

SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data.

Evguenia Kopylova, +2 more

- 01 Dec 2012 -

Bioinformatics

- Vol. 28, Iss: 24, pp 3211-3217

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.

Citations

PDF

Open Access

More filters

Journal ArticleDOI

Transcriptomics at Maize Embryo/Endosperm Interfaces Identifies a Transcriptionally Distinct Endosperm Subdomain Adjacent to the Embryo Scutellum.

Nicolas M. Doll, +13 more

- 21 Feb 2020 -

The Plant Cell

TL;DR: The detection of cell death in some EAS cells together with an accumulation of crushed cell walls suggests that the EAS is a dynamic zone from which cell layers in contact with the embryo are regularly eliminated and to which additional endosperm cells are recruited as the embryo grows.

...read moreread less

Journal ArticleDOI

Exploring the effects of operational mode and microbial interactions on bacterial community assembly in a one-stage partial-nitritation anammox reactor using integrated multi-omics

Yulin Wang, +9 more

- 28 Aug 2019 -

Microbiome

TL;DR: These findings provide the first insight that the bacterial communities in the PNA reactor are defined by not only abiotic factors (operating mode) but also metabolic interactions, such as nitrogen metabolism, exchange of electron donors, and auxotrophies.

...read moreread less

Journal ArticleDOI

Discrepant gene functional potential and cross-feedings of anammox bacteria Ca. Jettenia caeni and Ca. Brocadia sinica in response to acetate

Ying Feng, +6 more

- 15 Nov 2019 -

Water Research

TL;DR: The mechanism underlying discrepant responses of different anammox species to acetate is clarified, and a possible strategy for obtaining higher nitrogen removal rates in wastewater treatment under low C/N ratio is suggested.

...read moreread less

Journal ArticleDOI

Metagenomic and metatranscriptomic insights into the complex nitrogen metabolic pathways in a single-stage bioreactor coupling partial denitrification with anammox

Depeng Wang, +4 more

- 15 Oct 2020 -

Chemical Engineering Journal

TL;DR: The nitrogen metabolic network is established based on the comprehensive analyses of the abundance and mRNA expression of functional genes, which might improve the understanding of the nitrogen metabolic mechanisms of the combined partial-denitrification and anammox process.

...read moreread less

Journal ArticleDOI

Validating the Cyc2 Neutrophilic Iron Oxidation Pathway Using Meta-omics of Zetaproteobacteria Iron Mats at Marine Hydrothermal Vents.

Sean M. McAllister, +6 more

TL;DR: Investigating a promising possible iron oxidation gene, cyc2, in iron-rich hydrothermal vents, shows that Cyc2 is widespread among iron oxidizers and is highly expressed and potentially regulated, making it a good marker for the capacity for iron oxidation and potentially a marker for activity.

...read moreread less

Collapse

References

PDF

Open Access

More filters

Journal ArticleDOI

Basic Local Alignment Search Tool

Stephen F. Altschul, +4 more

- 01 Oct 1990 -

Journal of Molecular Biology

TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.

...read moreread less

Journal ArticleDOI

Fast and accurate short read alignment with Burrows–Wheeler transform

Heng Li, +1 more

- 01 Jul 2009 -

Bioinformatics

TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.

...read moreread less

Journal ArticleDOI

Search and clustering orders of magnitude faster than BLAST

Robert C. Edgar

- 01 Oct 2010 -

Bioinformatics

TL;DR: UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters and offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets.

...read moreread less

Journal ArticleDOI

ARB: a software environment for sequence data

Wolfgang Ludwig, +31 more

- 15 Mar 2004 -

Nucleic Acids Research

TL;DR: The ARB program package comprises a variety of directly interacting software tools for sequence database maintenance and analysis which are controlled by a common graphical user interface.

...read moreread less

Journal ArticleDOI

SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB

Elmar Pruesse, +6 more

- 01 Dec 2007 -

Nucleic Acids Research

TL;DR: SILVA (from Latin silva, forest), was implemented to provide a central comprehensive web resource for up to date, quality controlled databases of aligned rRNA sequences from the Bacteria, Archaea and Eukarya domains.

...read moreread less