RNAmmer protocols

RNAmmer specifications

Information


Unique identifier OMICS_03553
Name RNAmmer
Alternative name RNAHMMER
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Karin Lagesen <>

Publication for RNAmmer

RNAmmer IN pipelines

 (28)
2018
PMCID: 5769542
PMID: 29337314
DOI: 10.1038/sdata.2017.203

[…] of the hug, et al. phylogenetic marker set was constructed using the same parameters with only the alignments of the draft genomes for fig. 2., 16s rrna genes were predicted from draft genomes using rnammer34 (v1.2; parameters: -s bac -m ssu). 276 16s rrna genes were detected and aligned using the sina web portal aligner35 (https://www.arb-silva.de/aligner/). aligned 16s rrna gene sequences […]

2018
PMCID: 5834339
PMID: 29496843
DOI: 10.1128/genomeA.01487-17

[…] against the clusters of orthologous groups (cogs) database and the rapid annotations using subsystems technology (rast) web server (6). ribosomal rnas (5s, 16s, and 23s rrnas) were predicted using rnammer software (7)., the genome was 1,672,788-bp long, assembled in five scaffolds (seven contigs) with a g+c content of 36.9%. overall, 1,589 protein-coding sequences were identified, including […]

2017
PMCID: 5374242
PMID: 28360168
DOI: 10.1128/genomeA.00101-17

[…] blastp against the clusters of orthologous groups (cog) and the genbank databases. trna gene detection was performed using the trnascanse tool (7), whereas ribosomal rna genes were predicted using rnammer (8)., the genome from s. specialis strain gw41-1564t is 5,874,245 bp in length with a g+c content of 72.72%. after assembly, the genome is composed of 143 scaffolds (composed of 168 contigs). […]

2017
PMCID: 5658501
PMID: 29074663
DOI: 10.1128/genomeA.01183-17

[…] reads). the paired-end reads were assembled de novo using clc genomics workbench 4.8 (clc bio, denmark). structural rna predictions were determined by using trnascan-se 1.21 for trnas (2) and rnammer 1.2 for rna (3). prodigal version 2.60 was used to predict open reading frames (orfs) in the draft genome of microbacterium sp. strain sz1 (4). the assembled genome sequence was annotated […]

2017
PMCID: 5850609
PMID: 29220489
DOI: 10.1093/molbev/msx310

[…] resulting in 187 matched species. to control for shared ancestry in subsequent analyses, we constructed a phylogenetic tree based off the rrna sequences for this set of species. we first used rnammer to extract a randomly chosen 16s and 23s rrna sequence from each genome, followed by muscle (v3.8.31) on each individual rrna to produce a multiple-sequence alignments (edgar 2004). […]

RNAmmer institution(s)
Centre for Molecular Biology and Neuroscience and Institute of Medical Microbiology, University of Oslo, Oslo, Norway

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