RNAmmer protocols

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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

 (510)
2018
PMCID: 5764938
PMID: 29326214
DOI: 10.1128/genomeA.01422-17

[…] rs ii and illumina hiseq dna to determine the complete genomic sequence of the b. melitensis qh61. the annotation was performed using genemarks (), repeat masker (), trf (), trnascan-se (), and rnammer ()., the whole-genome sequence of b. melitensis qh61 was found to be 3,311,767 bp in size and to be composed of two circular chromosomes, chromosome i (2,126,173 bp) and chromosome ii […]

2018
PMCID: 5764942
PMID: 29326218
DOI: 10.1128/genomeA.01435-17

[…] annotations were performed by rapid annotation using subsystem technology (rast) (, ). trna gene detection was performed using the trnascan-se 2.0 tool (), whereas rrna genes were predicted using rnammer (). plasmid presence was checked by plasmidfinder software ()., after assembly, the two genomes were composed of 99 scaffolds. for strains l103 and c635, the total sizes were 2,193,610 bp, […]

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

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

2018
PMCID: 5773718
PMID: 29348333
DOI: 10.1128/genomeA.01418-17

[…] plasmid, pkap, of 41.7 kb (). the genome contains three rrna clusters in 16s-23s-5s configurations., gene annotation of the draft sequence was carried out using prodigal (), trnascan-se (), and rnammer () software tools. next to 36 trna genes, 1,080 protein coding sequences could be identified, of which, 787 could be functionally annotated by a similarity search against the eggnog database […]

2018
PMCID: 5786695
PMID: 29371369
DOI: 10.1128/genomeA.01565-17

[…] the ncbi nonredundant protein sequence (nr) database using blastp with an e value of 1 × 0.001, coverage of 0.7×, and 30% identity. noncoding genes and miscellaneous features were predicted using rnammer (), aragorn (), rfam (), pfam (), and infernal (). of the 7,084 predicted genes, 7,029 were protein-coding genes and 55 were rnas (namely, 3 5s rrnas, 1 16s rrna, 1 23s rrna, and 50 trnas). […]


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RNAmmer in publications

 (1159)
PMCID: 5946492
PMID: 29774049
DOI: 10.1186/s13068-018-1136-6

[…] rrna gene sequences was calculated by emirge based on the length-normalized read number of mapped reads. the presence of rrna gene sequences within each curated genome was identified using online rnammer 1.2 server with default parameters [], and then, the identified 16s rrna gene sequence was further annotated by blastn search against silva ssu 115 and greengenes (2013–5 release) databases […]

PMCID: 5943519
PMID: 29743638
DOI: 10.1038/s41598-018-24481-1

[…] anscripts as functional noncoding rnas, including microrna, trna, rrna, snorna, etc. in order to rule out this possibility, we blasted the sequences of candidate intergenic regions against rfam-11.0, rnammer-1.2, snorna-lbme-db, mirbase19, and gtrnadb database to filter out regions harboring potential functional noncoding rnas. intragenic regions passing the filtering criteria are listed in table  […]

PMCID: 5940233
PMID: 29738547
DOI: 10.1371/journal.pone.0196995

[…] described in song et al., 2016 [] using ‘bacteria and archaea (11)’ genetic code and the ncbi database for non-redundant (nr) protein sequences. to search the ribosomal rna sequences, we applied rnammer v1.2 server [] using the option of bacteria, and then re-confirmed by blastn. introns, trnas, and other small rna were searched by aragorn [] and rfam cmscan v1.1 []. several important genes […]

PMCID: 5945888
PMID: 29780362
DOI: 10.3389/fmicb.2018.00793

[…] the non-redundant protein sequences database. transfer rnas (trnas) were identified using trnascan-se (v1.23, http://lowelab.ucsc.edu/trnascan-se) and ribosome rnas (rrnas) were determined using rnammer (v1.2, http://www.cbs.dtu.dk/services/rnammer/). dnaman was used to calculate molecular masses and isoelectric points for predicted phage proteins. the whole viral nucleotide sequence […]

PMCID: 5936029
PMID: 29728057
DOI: 10.1186/s12864-018-4668-z

[…] on refseq protein, swissprot and ensembl protein reference files from apis mellifera and metaseiulus occidentalis to retrieve the corresponding annotations. the contigs were also processed with rnammer (standard parameters, version 1.2) [] to find ribosomal genes, with repeatmasker (−engine crossmatch -gccalc -species varroa destructor parameters, version open-4-0-3) [] to list […]


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

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