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.

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