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RNAprob specifications

Information


Unique identifier OMICS_18576
Name RNAprob
Software type Framework/Library
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS
Programming languages C
Computer skills Advanced
Stability Stable
Maintained Yes

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  • person_outline Sharon Aviran <>

Publication for RNAprob

RNAprob in publications

 (7)
PMCID: 5758915
PMID: 29177466
DOI: 10.1093/nar/gkx1057

[…] an rna because of thermal fluctuations. we also benchmarked rsample for sequences that populate a single structure, and its performance was similar to other methods that can use shape data: rme (), rnaprob (), rnaprobing (), rnasc () and rnastructure fold ()., an overview of rsample is shown in figure . the procedure uses two partition function calculations to model structure (,). a partition […]

PMCID: 5113702
PMID: 27503141
DOI: 10.1002/wrna.1378

[…] database of protein sequences. with the same approach, pprint combines evolutionary information from pssms with svms, thus predicting rna‐binding sites with an accuracy of 0.81. similarly, rnaprob employs a smoothed pssm encoding scheme to predict rna‐binding sites on proteins and shows an accuracy of 0.89. slightly different types of physicochemical properties are combined […]

PMCID: 4661811
PMID: 26540053
DOI: 10.3390/ijms161125952

[…] risp, which is a hybrid rna-binding site predictor which uses svms in conjunction with pssms and achieved a 61.0% increase in sensitivity and an 83.3% increase in specificity. a similar method, rnaprob, using svm and a novel smoothed pssm encoding method, was developed by cheng et al. [] and it gave better performance than the then current state-of-the-art systems. in 2010, li et al. [] […]

PMCID: 4595337
PMID: 26439842
DOI: 10.1371/journal.pone.0139731

[…] disordered nature of a protein may offer an additional layer of information that can complement and enhance the performance of rna-binding site prediction software, such as rnabindr [], naps[] or rnaprob[], even though some of these methods already take evolutionary information into account. while the accuracy of these tools is progressively getting higher, it was shown recently […]

PMCID: 3795737
PMID: 24146760
DOI: 10.1371/journal.pone.0075542

[…] time to generate position-specific scoring matrix (pssm) in homology extension. the homology extension procedure has been intensively used in many bioinformatics software, i.e., psipred , memsat3 , rnaprob , psi-coffee , and etc. however, the effects of database sizes and sequence identities on prediction accuracy have not been fully investigated. the speed of a prediction procedure […]


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RNAprob institution(s)
Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, CA, USA
RNAprob funding source(s)
Supported by National Institutes of Health (NIH) grants: HG006860 from the National Human Genome Research Institute (NHGRI)-NIH and T32-GM008799 from The National Institute of General Medical Sciences (NIGMS)-NIH.

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