NEIL (Nucleotide Expression, Inspiration, and Logic): a new Computational Approach to the Analysis of MicroRNA-Related Nucleotide Variations

Abstract

Genetic variations of microRNAs and their target sites among individuals are increasingly recognized as possible factors underlying various human disorders. Currently, the computer-assisted predictions of microRNA-binding sites rely exclusively on one or few reference genomic sequences and do not take into consideration significant variations within human genomes. There is a need to develop computational approaches to assess the probability of excessively strong or completely disabled microRNA-binding sites upon the known SNP frequencies. We developed the software NEIL to align the individual microRNA and mRNA sequences in the setting of the corresponding genomic SNP map of the targeted gene. This approach allows us to visualize the presence of SNPs within and in the proximity of microRNA-target sites in order to predict the combinatorial effects of SNPs on microRNA-mRNA binding and the expression of the microRNA-regulated genes.

"An Excel Macro Code for the Analysis of the Density and Distance between the Homologous microRNA-Binding Sites"

“…The computer-assisted prediction of microRNA-binding sites upon the reference genomic sequences does not reckon with the well-known by now genomic variation, which is characteristic of all biological species [1]. We developed the miRNA-mRNA complementarity alignment tool NEIL [2], and the more complex package called miRNAhrend [3] (https://franziskaahrend.pythonanywhere.com/). The latter one is the online-available package for the prediction and visualization of the miRNA-binding sites in any RNA sequence with their following verification by the complementarity alignment.…”