QRNA statistics

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Citations per year

Number of citations per year for the bioinformatics software tool QRNA
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Tool usage distribution map

This map represents all the scientific publications referring to QRNA per scientific context
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Associated diseases

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Popular tool citations

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Protocols

QRNA specifications

Information


Unique identifier OMICS_15802
Name QRNA
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Source code URL http://eddylab.org/software/rnabob/rnabob.tar.gz
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Elena Rivas

Publication for QRNA

QRNA citations

 (54)
library_books

Identification of 15 candidate structured noncoding RNA motifs in fungi by comparative genomics

2017
BMC Genomics
PMCID: 5640933
PMID: 29029611
DOI: 10.1186/s12864-017-4171-y

[…] mong structural elements that are only poorly conserved at the nucleotide level []. As a result, some successful computational search strategies for structured ncRNA candidates use algorithms such as QRNA [], RNAz [], or CMfinder [], which search for nucleotide covariation or other evidence of structure formation and conservation, rather than just searching for conserved sequence. A computational […]

library_books

Genome Wide Detection of Small Regulatory RNAs in Deep Sea Bacterium Shewanella piezotolerans WP3

2017
Front Microbiol
PMCID: 5471319
PMID: 28663744
DOI: 10.3389/fmicb.2017.01093

[…] QRNA, A tool used for the detection of the conserved RNA secondary structures, including both ncRNA genes and cis-regulatory RNA structures.RNAz, A program for predicting structurally conserved and th […]

library_books

A Review on Recent Computational Methods for Predicting Noncoding RNAs

2017
Biomed Res Int
PMCID: 5434267
PMID: 28553651
DOI: 10.1155/2017/9139504

[…] ogy-based methods is introduced based on structure conservations. Instead of sequence alignment, these methods use RNA secondary structure alignment to measure RNA similarity. Popular methods include QRNA [] and RNAz []. Specifically, QRNA compares query RNA with known RNAs using “three probabilistic pair-grammars: a pair stochastic context-free grammar modeling alignments constrained by structura […]

library_books

An improved method for identification of small non coding RNAs in bacteria using support vector machine

2017
Sci Rep
PMCID: 5382675
PMID: 28383059
DOI: 10.1038/srep46070

[…] hand, zMFold was efficient in identifying positive, but not negative sRNAs. As a result, these methods generated either a high number of false negatives (FN) or false positives (FP). Other tools like QRNA and the one proposed by Arnedo et al. showed slightly better performance for the identification of both positive and negative sRNAs simultaneously, but their accuracies were less than optimums.In […]

library_books

A Review of Computational Methods for Finding Non Coding RNA Genes

2016
Genes
PMCID: 5192489
PMID: 27918472
DOI: 10.3390/genes7120113

[…] sults compare favorably when tested on known RNAs from BLASTN queries []. McCutcheon et al. [] extended this work with experimental characterization. In addition to having a high false positive rate, QRNA fails to identify ncRNAs without significant structure while also picking up cis-regulatory mRNA structures. The results illustrate the importance of having multiple genome sequences at various e […]

library_books

Bacterial small RNAs in the Genus Rickettsia

2015
BMC Genomics
PMCID: 4683814
PMID: 26679185
DOI: 10.1186/s12864-015-2293-7

[…] nd widely used programs to identify potential transcription factor binding sites [–]; Rho-independent terminators using RNAMotif [], TransTermHP [], and FindTerm []; conserved secondary structures by QRNA []; and conserved nucleotide sequences by BLASTN 2.0 []. Further, this program has been widely applied for sRNA predictions in several other bacteria attesting to its potential for accurately pre […]


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QRNA institution(s)
Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
QRNA funding source(s)
This work was partially supported by a postdoctoral grant from the Sloan Foundation, by the Howard Hughes Medical Institute and the NIH National Human Genome Research Institute.

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