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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 citations

 (1373)
library_books

Bioreactor microbial ecosystems with differentiated methanogenic phenol biodegradation and competitive metabolic pathways unraveled with genome resolved metagenomics

2018
Biotechnol Biofuels
PMCID: 5946492
PMID: 29774049
DOI: 10.1186/s13068-018-1136-6

[…] 16S 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 at […]

library_books

Plastid genome analysis of three Nemaliophycidae red algal species suggests environmental adaptation for iron limited habitats

2018
PLoS One
PMCID: 5940233
PMID: 29738547
DOI: 10.1371/journal.pone.0196995

[…] dure 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 a […]

call_split

Characterization and Genomic Study of Phage vB_EcoS B2 Infecting Multidrug Resistant Escherichia coli

2018
Front Microbiol
PMCID: 5945888
PMID: 29780362
DOI: 10.3389/fmicb.2018.00793
call_split See protocol

[…] inst 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 similari […]

library_books

Transcriptome profiling of the honeybee parasite Varroa destructor provides new biological insights into the mite adult life cycle

2018
BMC Genomics
PMCID: 5936029
PMID: 29728057
DOI: 10.1186/s12864-018-4668-z

[…] 1e-5) 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 the contained […]

library_books

Genome Sequencing and Analysis of the Peanut B Genome Progenitor (Arachis ipaensis)

2018
Front Plant Sci
PMCID: 5943715
PMID: 29774047
DOI: 10.3389/fpls.2018.00604

[…] aligned A. ipaensis genome assembly to against the Rfam databese (version 12.1) (Nawrocki et al., ). The pre-tRNAs were identified using tRNAscan-SE (Lowe and Eddy, ), pre-rRNAs were predicted using RNAmmer (Lagesen et al., ), pre-snRNAs were annotated using INFERNAL (Nawrocki et al., ) and others were also obtained by BLAST search against the Rfam database.The RepeatMasker (Chen, ), RepeatProtei […]

library_books

Draft Genome Sequence of Paucibacter aquatile CR182T, a Strain with Antimicrobial Activity Isolated from Freshwater of Nakdong River in South South Korea

2018
Genome Announc
PMCID: 5920192
PMID: 29700134
DOI: 10.1128/genomeA.00194-18

[…] oups of proteins (COG) () databases. Signal peptides and transmembrane helices were predicted using SignalP 4.1 () and TMHMM v2.0 (). rRNA, tRNA, and other miscellaneous features were predicted using RNAmmer v1.2 (), tRNAscan-SE v1.21 (), and Rfam v12.0 ().The draft genome sequence of P. aquatile CR182T is 5,523,543 bp, with a G+C content of 66.3%. The genome is predicted to have 4,544 coding sequ […]

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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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