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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

 (17)
library_books

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

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

[…] model (this model was selected on the basis of the test by prottest []) and a bootstrap replication number of 500., 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, […]

library_books

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

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

[…] 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

Dietary energy drives the dynamic response of bovine rumen viral communities

2017
PMCID: 5704599
PMID: 29179741
DOI: 10.1186/s40168-017-0374-3

[…] to identify and remove prefix duplicates of length 80 bp., cellular contamination of viral and deep viral metagenomes was estimated from 16s and 23s rrna gene sequences detected by the standalone meta_rna software []., all reads within a dataset (microbial, viral, and deep viral) were assembled independently with spades [] using unpaired reads as input (k-mer lengths of 21, 33, 55, 77, 99, […]

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

[…] by quality trimming using trimmomatic (; v.0.33 ; pe slidingwindow:10:28 minlen:75)., 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
PMCID: 5673642
PMID: 29163419
DOI: 10.3389/fmicb.2017.02131

[…] 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., in order to estimate […]

library_books

Microbiome overview in swine lungs

2017
PMCID: 5515459
PMID: 28719637
DOI: 10.1371/journal.pone.0181503

[…] were used to analyze the taxonomic distribution of each read hit. first, mg-rast server [] using the lowest common ancestor (lca) method and megan4 [], both with default parameters, were applied. meta-rna software was employed to perform 16s rrna identification []. secondly, the metagenomics (mg) workflow [] was applied, which performed different mappings restraining subsets of reads […]


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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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