meta_rna statistics

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Citations per year

Number of citations per year for the bioinformatics software tool meta_rna
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Tool usage distribution map

This map represents all the scientific publications referring to meta_rna per scientific context
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Associated diseases

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Protocols

meta_rna specifications

Information


Unique identifier OMICS_10285
Name meta_rna
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Windows
Programming languages Python
Computer skills Advanced
Stability Stable
Requirements
HMMER
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Weizhong Li

Publication for meta_rna

meta_rna citations

 (26)
library_books

Genome Reduction in Psychromonas Species within the Gut of an Amphipod from the Ocean’s Deepest Point

2018
mSystems
PMCID: 5893861
PMID: 29657971
DOI: 10.1128/mSystems.00009-18

[…] Psychromonas 16S rRNA genes were recovered from the gut metagenomes with the Meta-RNA program (). Alignment of nearly full-length (>1,400 bp) 16S rRNA genes was conducted in MEGA (version 7.0.21) () with the MUSCLE algorithm by using a gap open penalty of −50, the unweighted p […]

library_books

High Prevalence of Quorum Sensing and Quorum Quenching Activity among Cultivable Bacteria and Metagenomic Sequences in the Mediterranean Sea

2018
Genes
PMCID: 5852596
PMID: 29462892
DOI: 10.3390/genes9020100

[…] pendently using IDBA-UD []. The genes obtained on the assembled contigs were predicted using Prodigal [] transfer RNA (tRNA), and the rRNA genes were predicted using tRNAscan-LE [], ssu-align [], and meta-rna []. A taxonomic and functional annotation was performed comparing the predicted protein sequences against NCBI NR, COG [], and TIGFRAM [] databases were performed using USEARCH6 []. USEARCH6 […]

library_books

A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer

2017
PMCID: 5739024
PMID: 29099490
DOI: 10.1038/ismej.2017.187

[…] From the high-quality paired-end Illumina sequencing reads, 16S rRNA gene fragments were identified using Meta-RNA (; v.H3; -e 1e-10). Putative rRNA fragments and associated mate pairs from each sample were processed through EMIRGE (, ); emirge_amplicon.py; -l 113 -i 163 -s 33 -a 32 —phred33) to generate […]

library_books

Reconstruction of Diverse Verrucomicrobial Genomes from Metagenome Datasets of Freshwater Reservoirs

2017
Front Microbiol
PMCID: 5673642
PMID: 29163419
DOI: 10.3389/fmicb.2017.02131

[…] ne predictions on the assembled contigs were assessed using Prodigal in metagenomic mode (), tRNAs were predicted using tRNAscan-SE (), and ribosomal rRNA genes were identified using ssu-align () and meta-rna (). Comparisons of predicted protein sequences against NCBI NR, COG (), and TIGFRAM () databases were performed for taxonomic binning and functional annotation. […]

library_books

Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics

2017
Nat Commun
PMCID: 5636890
PMID: 29021524
DOI: 10.1038/s41467-017-01086-2

[…] To identify potential eukaryote hosts for the newly assembled virophages, Lake Mendota and Trout Bog Lake metagenomic contigs were searched for 18S sequences (using meta-RNA, E value ≤ 0.01). Because no pre-filtering step was included in the sampling protocol, eukaryote genomes should be sequenced alongside other microbial and viral genomes; however, they should […]

library_books

Genome diversity of marine phages recovered from Mediterranean metagenomes: Size matters

2017
PLoS Genet
PMCID: 5628999
PMID: 28945750
DOI: 10.1371/journal.pgen.1007018

[…] l metagenomes were assembled using IDBA-UD []. The resulting genes on the assembled contigs were predicted using Prodigal []. tRNA and rRNA genes were predicted using tRNAscan-SE [], ssu-align [] and meta-rna []. Predicted protein sequences were compared against NCBI NR, COG [] and TIGRFAM [] databases using USEARCH6 [] for taxonomic and functional annotation. GC content was calculated using the G […]


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meta_rna institution(s)
California Institute for Telecommunications and Information Technology, University of California, La Jolla, San Diego, CA, USA
meta_rna funding source(s)
Gordon and Betty Moore Foundation (CAMERA project)

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