Improving model predictions for RNA interference activities that use support vector machine regression by combining and filtering features

Peek, Andrew S.

doi:10.1186/1471-2105-8-182

Cited by 39 publications

(34 citation statements)

References 67 publications

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“…Now we have developed VIRsiRNApred -a viral siRNA efficacy prediction algorithm. Although many mammalian siRNA prediction algorithms have been developed in the past [33], these methods either classify a siRNA as effective/non-effective [29] or predict the inhibition efficacy of a siRNA [31,32]. However, there is limited success in predicting siRNA efficacy due to limited size and diversity of available siRNA datasets [50].…”

Section: Discussionmentioning

confidence: 99%

VIRsiRNApred: a web server for predicting inhibition efficacy of siRNAs targeting human viruses

2013

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BackgroundSelection of effective viral siRNA is an indispensable step in the development of siRNA based antiviral therapeutics. Despite immense potential, a viral siRNA efficacy prediction algorithm is still not available. Moreover, performances of the existing general mammalian siRNA efficacy predictors are not satisfactory for viral siRNAs. Therefore, we have developed “VIRsiRNApred” a support vector machine (SVM) based method for predicting the efficacy of viral siRNA.MethodsIn the present study, we have employed a new dataset of 1725 viral siRNAs with experimentally verified quantitative efficacies tested under heterogeneous experimental conditions and targeting as many as 37 important human viruses including HIV, Influenza, HCV, HBV, SARS etc. These siRNAs were divided into training (T1380) and validation (V345) datasets. Important siRNA sequence features including mono to penta nucleotide frequencies, binary pattern, thermodynamic properties and secondary structure were employed for model development.ResultsDuring 10-fold cross validation on T1380 using hybrid approach, we achieved a maximum Pearson Correlation Coefficient (PCC) of 0.55 between predicted and actual efficacy of viral siRNAs. On V345 independent dataset, our best model achieved a maximum correlation of 0.50 while existing general siRNA prediction methods showed PCC from 0.05 to 0.18. However, using leave one out cross validation PCC was improved to 0.58 and 0.55 on training and validation datasets respectively. SVM performed better than other machine learning techniques used like ANN, KNN and REP Tree.ConclusionVIRsiRNApred is the first algorithm for predicting inhibition efficacy of viral siRNAs which is developed using experimentally verified viral siRNAs. We hope this algorithm would be useful in predicting highly potent viral siRNA to aid siRNA based antiviral therapeutics development. The web server is freely available at http://crdd.osdd.net/servers/virsirnapred/.

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Section: Discussionmentioning

confidence: 99%

VIRsiRNApred: a web server for predicting inhibition efficacy of siRNAs targeting human viruses

2013

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“…siVirus provides siRNA sequences directed against conserved regions of viruses like HIV, HCV, INFV, and SARS‐CoV with minimum off‐target effects . Although many machine learning techniques like boosted genetic programming, artificial neural network, and support vector machine have been used to design mammalian siRNAs, however, their performances were not satisfactory for viral siRNAs. This may be due to the fact that these methods were not trained on viral siRNAs.…”

Section: Bioinformatics Resourcesmentioning

confidence: 99%

A review on current status of antiviral siRNA

Qureshi

Tantray

Kirmani

et al. 2018

Reviews in Medical Virology

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Viral diseases like influenza, AIDS, hepatitis, and Ebola cause severe epidemics worldwide. Along with their resistant strains, new pathogenic viruses continue to be discovered so creating an ongoing need for new antiviral treatments. RNA interference is a cellular gene-silencing phenomenon in which sequence-specific degradation of target mRNA is achieved by means of complementary short interfering RNA (siRNA) molecules. Short interfering RNA technology affords a potential tractable strategy to combat viral pathogenesis because siRNAs are specific, easy to design, and can be directed against multiple strains of a virus by targeting their conserved gene regions. In this review, we briefly summarize the current status of siRNA therapy for representative examples from different virus families. In addition, other aspects like their design, delivery, medical significance, bioinformatics resources, and limitations are also discussed.

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“…These three tools assist in the design of effective siRNAs, as there are several properties that discriminate between effective and ineffective siRNA duplexes (46,47). The ddRNAi tool helps to design siRNAs, which are expressed directly from DNA transfected into cells to make the siRNA (48–50).…”

Section: Online Toolsmentioning

confidence: 99%

IDT SciTools: a suite for analysis and design of nucleic acid oligomers

Owczarzy

Tataurov

et al. 2008

Nucleic Acids Research

412

258

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DNA and RNA oligomers are used in a myriad of diverse biological and biochemical experiments. These oligonucleotides are designed to have unique biophysical, chemical and hybridization properties. We have created an integrated set of bioinformatics tools that predict the properties of native and chemically modified nucleic acids and assist in their design. Researchers can select PCR primers, probes and antisense oligonucleotides, find the most suitable sequences for RNA interference, calculate stable secondary structures, and evaluate the potential for two sequences to interact. The latest, most accurate thermodynamic algorithms and models are implemented. This free software is available at http://www.idtdna.com/SciTools/SciTools.aspx.

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Improving model predictions for RNA interference activities that use support vector machine regression by combining and filtering features

Cited by 39 publications

References 67 publications

VIRsiRNApred: a web server for predicting inhibition efficacy of siRNAs targeting human viruses

VIRsiRNApred: a web server for predicting inhibition efficacy of siRNAs targeting human viruses

A review on current status of antiviral siRNA

IDT SciTools: a suite for analysis and design of nucleic acid oligomers

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