QRNA protocols

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QRNA specifications


Unique identifier OMICS_15802
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


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  • person_outline Elena Rivas <>

Publication for QRNA

QRNA in pipelines

PMCID: 5192489
PMID: 27918472
DOI: 10.3390/genes7120113

[…] 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 […]

PMCID: 2248559
PMID: 18226231
DOI: 10.1186/1471-2105-9-61

[…] opteron 64 bit machines., a standard technique for discovering new rnas, in the absence of queries, is to align genomic fragments and search the alignment for significant structural conservation. qrna [] rnaz [] and msari [] are some well-known programs frequently used for this purpose. their performance, of course depends upon the underlying sequence alignments. our work here suggests […]

PMCID: 2443716
PMID: 18577217
DOI: 10.1186/1471-2148-8-182

[…] the 5' part of the closest gene in the correct orientation and the genomic region matching to the glgi fragment to a genescan prediction. the coding potential of the transcripts was assessed using qrna program []., to identify the 5' boundaries of the novel glgi sequences, we performed 5' race (rapid amplification of cdna ends) using generacer race ready cdna kit (invitrogen, carlsbad, ca). […]

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QRNA in publications

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

[…] 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 […]

PMCID: 5471319
PMID: 28663744
DOI: 10.3389/fmicb.2017.01093

[…] shown to act as cold regulated srnas. our study provided additional evidence at the transcriptional level to decipher the microbial adaptation mechanisms to extreme environmental conditions., 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 […]

PMCID: 5434267
PMID: 28553651
DOI: 10.1155/2017/9139504

[…] 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 […]

PMCID: 5382675
PMID: 28383059
DOI: 10.1038/srep46070

[…] srnas., several computational methods were developed in the recent past for the identification of srnas in bacteria using comparative genomics, primary sequence and secondary structure features. qrna used pairwise alignments to identify novel srnas in bacteria. this technique employed a pair hidden markov models (pair-hmms) and a pair stochastic context-free grammar (pair-scfg) to find […]

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

[…] 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 […]

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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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