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

Background:

Datasets:

VIRsi-RNAdb:

19mer

$V^{345}$: 345 sequences for validation

$T^{1380}$: 1380 sequences for training

Method:

SVM,ANN,KNN,REP Tree

siRNA sequence features:

Nucleotide Frequencies:is the number of each nucleotide in a siRNA,the objective of calculating nucleotide frequencies of siRNA sequences is to transfrom any length of nucleotide sequence to fixed length feature vectors.

Binary Pattern: A : 1000, G : 0010 , C : 0100 , U : 0001

Thermodynamic Properties : correspond to the Gibbs free energy stability of the nucleotide pairs of siRNAs

Secondary Structure :

Hybrid Approaches:

Leave one out cross validation(LOOCV):

Viral siRNA target conservation : use ALIGN0 algorithm

Algorithm and server implementation SVM:

we used the radial basis function kernel (RBF):

$\bar{x}$and$\bar{y}$ are two data vectors , and $\gamma$ is a training parameter

$$k(\bar{x},\bar{y})=\exp (-\gamma ||\bar{x}-\bar{y}|{|}^2)$$

$n$ is the size of test set

Pearson’s correlation coefficient®:

$E_i^{pred}$ and $E_i^{act}$ is the predict and actual efficacy respectively

$$R=\frac{n{\sum }_{n=1}^n{E}_i^{act}{E}_i^{pred}-{\sum }_{n=1}^n{E}_i^{act}{\sum }_{n=1}^n{E}_i^{pred}}{\sqrt{n{\sum }_{n=1}^n(E_i^{act}{)}^2-({\sum }_{n=1}^n{E}_i^{act}{)}^2}\sqrt{n{\sum }_{n=1}^n(E_i^{pred}{)}^2-({\sum }_{n=1}^n{E}_i^{pred}{)}^2}}$$

using heterogeneous siRNA dataset and using mammalian homogeneous siRNA dataset

Conclusion:

SVM is better than existing siRNA prediction algorithm

the first viral siRNA effi- cacy prediction algorithm developed on experimentally verified viral siRNAs targeting as many as 37 diverse human viruses since existing general mammalian siRNA prediction methods are not able to effectively predict viral siRNA activity.