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RNAcentral specifications

Information


Unique identifier OMICS_05585
Name RNAcentral
Restrictions to use None
Community driven No
Data access File download, Browse, Application programming interface
User data submission Not allowed
Version 10
Maintained Yes

Publications for RNAcentral

RNAcentral citations

 (14)
library_books

Linking the Effect of Antibiotics on Partial Nitritation Biofilters: Performance, Microbial Communities and Microbial Activities

2018
Front Microbiol
PMCID: 5834488
PMID: 29535704
DOI: 10.3389/fmicb.2018.00354

[…] with an e-value < 10-10 were removed from the analysis. Then, an additional screening to eliminate other non-coding RNA sequences was done by BLAST search against non-coding RNA databases offered by RNACentral. After the removal of non-coding RNA, the remaining sequences were thus considered mRNA.The mRNA sequences were then BLASTed against several reference databases of genomes derived from RefS […]

library_books

Genetic variation associated with healthy traits and environmental conditions in Vaccinium vitis idaea

2018
BMC Genomics
PMCID: 5748963
PMID: 29291734
DOI: 10.1186/s12864-017-4396-9

[…] eve gene ontology (GO) terms associated to the hits obtained after the BLASTX search. GO terms assigned were restricted to the plant slim GO subset. Additionally, we searched for similar sequences in RNAcentral [] (release 7), a comprehensive database of non-coding RNA sequences, using nhmmer [] with an E-value <0.001 and all other parameters set to default values. […]

call_split

Identification of metastasis associated microRNAs in serum from rectal cancer patients

2017
Oncotarget
PMCID: 5685733
PMID: 29163812
DOI: 10.18632/oncotarget.21412
call_split See protocol

[…] computed by summing the total read count per sequence (isomiR) overlapping each miRNA locus. Mature miRNAs and non-coding RNAs were annotated using miRBase (Release 21, 2014) and RNA Central (http://rnacentral.org) respectively. IsomiR variants were detected using SeqBuster [] combined with a panel of in-house perl and R-scripts, which are available upon request. IsomiRs with mismatches to the ge […]

call_split

A general mechanism of ribosome dimerization revealed by single particle cryo electron microscopy

2017
Nat Commun
PMCID: 5620043
PMID: 28959045
DOI: 10.1038/s41467-017-00718-x
call_split See protocol

[…] The structural modeling was started by rigid-body fitting the B. subtilis structure (PDB-code 3J9W) in the density map in COOT. RNA sequences for L. lactis were taken from the RNAcentral database (http://rnacentral.org) and models were built using the B. subtilis ribosome as a template. The RNA was adjusted manually and subsequently refined using ERRASER. The protein models […]

library_books

The Huperzia selago Shoot Tip Transcriptome Sheds New Light on the Evolution of Leaves

2017
Genome Biol Evol
PMCID: 5622374
PMID: 28957460
DOI: 10.1093/gbe/evx169

[…] tes. Blobtools was run based on four blast (Version 2.4.0+) searches: a blastn megablast on the NCBI nucleotide database, a blastx on the SwissProt database, a blastn megablast on the SILVA database (RNAcentral SILVA collection) and a blastx search against NR (NCBI). The reads were remapped on the final transcriptome (63,908 contigs). The read_cov plot (; Supplementary Material Online) shows that […]

library_books

PARTICLE triplexes cluster in the tumor suppressor WWOX and may extend throughout the human genome

2017
Sci Rep
PMCID: 5541130
PMID: 28769061
DOI: 10.1038/s41598-017-07295-5

[…] leotides) in human was previously reported. Mouse PARTICLE (gene synonym 4930414L22RiK, 1933 nucleotides) was identified from a reference genome assembly. Comparison of human and mouse PARTICLE using RNAcentral (RNAcentral.org) revealed 55.7% coverage (797/1432 nucleotides) with 59.2% identity between their nucleotide sequences with the likelihood of finding this alignment by chance highly improba […]

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RNAcentral institution(s)
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK; Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland; [...]
RNAcentral funding source(s)
Supported by Biotechnology and Biological Sciences Research Council (BBSRC) [BB/N019199/1].

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