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ncRNAdb specifications

Information


Unique identifier OMICS_20734
Name ncRNAdb
Alternative name Noncoding RNAs database
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Maciej Szymanski

Publication for Noncoding RNAs database

ncRNAdb citations

 (9)
library_books

Molecular Characterization of Peripheral Extracellular Vesicles in Clinically Isolated Syndrome: Preliminary Suggestions from a Pilot Study

2017
PMCID: 5635803
PMID: 29099035
DOI: 10.3390/medsci5030019

[…] nces and poly-A using cutadapt []. After pre-processing, read-length distribution is computed and reads >15 nucleotides were aligned against a non-redundant non-coding RNA (ncRNA) reference database (ncRNAdb http://ncRNAdb.ba.itb.cnr.it) that collects and integrates sequences and annotations of various ncRNA classes such as micro RNA (miRNA), piwi-interacting RNA (piRNA), tRNA, small nucleolar RNA […]

library_books

An integrative framework to identify cell death related microRNAs in esophageal squamous cell carcinoma

2016
Oncotarget
PMCID: 5302951
PMID: 27462775
DOI: 10.18632/oncotarget.10779

[…] mation for experimentally identified miRNAs and their targets in cell death network. Now it has evolved into the updated version of ncRDeathDB (www.rna-society.org/ncrdeathdb) []. As of January 2015, ncRNADB provided over one thousand human miRNAs-targets entries, which were used in this study. Genes annotated in Gene Ontology (GO) term ‘apoptotic process’ (GO:0006915) and ‘autophagy’ (GO:0006914) […]

library_books

Use of RNA sequencing to evaluate rheumatic disease patients

2015
PMCID: 4488125
PMID: 26126608
DOI: 10.1186/s13075-015-0677-3

[…] er from the ones used for DE analysis of genes/transcripts. After the reads are aligned against the reference genome, non-coding annotations are used, such as the miRBase (database of known miRNAs), lncRNAdb (database of lncRNAs), ncRNAdb (database of non-coding regulatory RNAs) and others. Related third party analysis tools for this purpose include mirRanalyzer [], miRTools [], and lncRScan []. S […]

library_books

Comprehensive Reconstruction and Visualization of Non Coding Regulatory Networks in Human

2014
Front Bioeng Biotechnol
PMCID: 4261811
PMID: 25540777
DOI: 10.3389/fbioe.2014.00069

[…] above. The documentation is provided as JavaDoc at ncRNA-DB web site. Alternately, users may adopt the GraphAPI of OrientDB. The source code of CLI interface is available at https://code.google.com/p/ncrnadb/. […]

library_books

High throughput sequencing of small RNA transcriptomes reveals critical biological features targeted by microRNAs in cell models used for squamous cell cancer research

2013
BMC Genomics
PMCID: 3870990
PMID: 24160351
DOI: 10.1186/1471-2164-14-735

[…] s from databases designated by NRDR [] as containing miRNAs. Sequences from 15 different databases were included [], miRBase [], miRNAMap [], microRNA.org [], Argonaute, ASRP [], CSRDB [], fRNAdb [], ncRNAdb [], NONCODE [], RFAM [], RNAdb [], smiRNAdb [], TarBase [], UCSC Genome Browser human miRNAs []. Similarity search was performed using WU-BLAST v.2.2.6 with the DUST filter turned on, wordsize […]

library_books

Whole genome sequencing of the fish pathogen Francisella noatunensis subsp. orientalis Toba04 gives novel insights into Francisella evolution and pathogenecity

2012
BMC Genomics
PMCID: 3532336
PMID: 23131096
DOI: 10.1186/1471-2164-13-598

[…] We used the prokaryotic annotation pipeline from TIGR to annotate the genome: Glimmer 3 [] was used to predict the genes in the genome. NcRNAdb [] and RNammer [] was used to predict 23s and 16s RNA genes. tRNAscan-SE [] was used to predict tRNAs present in the genome. We used TMHMM [] to predict transmembrane helices and SignalP [] to […]

Citations

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ncRNAdb institution(s)
Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Poznan, Poland; Institute fur Chemie/Biochemie, Freie Universitat Berlin, Berlin, Germany
ncRNAdb funding source(s)
Supported by grants from the Polish State Committee for Scientific Research; the Fonds der Chemischen Industrie e.V.; and the National Foundation for Cancer Research.

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