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µLIVE web server provides virologists a simple web interface to design human-specific microRNA response elements (MREs). There MREs could be incorporated into the open reading frames (ORFs) of RNA viral sequences to increase attenuation and improve safety for the live attenuated virus (LAV) vaccines, based on miRNA-mediated gene silencing [1].

The steps to design an effective MRE includes (1) miRNA-target site prediction by miranda [2] and (2) iterative interactive site mutation with scores recalculation. The predicted target sites menu allows users to explore and design MREs for the pre-processed miRNA-target site prediction by miranda for all human miRNAs and ORFs of seven RNA viruses.

Note : If you use microLIVE for your research, please cite:
Duangdao Wichadakul, Wuttichai Mhuantong, Anan Jongkaewwattana and Supawadee Ingsriswang (2012), "A computational tool for the design of live attenuated virus vaccine based on microRNA-mediated gene silencing", BMC Genomics, 13: (Suppl 7):S15, [Web link].

The data sets used in our web server were compiled from two sources:

(1) 1,024 human mature miRNAs from miRBase release 16.0 [Sep/2010].

(2) 75,784 virus sequences from 7 viruses from NCBI [downloaded on Aug/26/2010].

Figure 1: To design microRNA response elements (MREs) for a set of RNA viral sequences, users need to (1) select a specifc human miRNA of interest, (2) input or upload viral RNA sequences in FASTA format, and (3) decide the input parameters for miRNA-target prediction. Then, click on "Submit" button. This figure presents sequences from Example 1.
Figure 2: The output of miRNA-taget prediction consists of three main sections: (1) "Input view" summerizing the parameters input by users, (2) "Alignment view" visualizing the multiple sequence alignment of input sequences, and (3) "Target view" listing the input sequences having target sites of the select miRNA, predicted by miranda [2].

The click on "View sequence and detail" button 2A will open a new window (Figure 3) displaying the selected sequence with highlighted target site(s).
A target site with higher binding score, lower binding energy, and located on a conserved region in the multiple sequence alignment could be used by users to design an effective MRE by clicking on the "Design MREs" button 2B. This will open a new window (Figure 4) for users to mutate the target site and recalculate scores. The mutated target site with low numbers of amino acid substitutions and modifications, higher binding score, and lower binding energy could be exported by users as an effective MRE for sequence mutation in wet-lab experiments. Clicking on "See other miRNAs that target the same binding site" button 2C will open a new window (Figure 5) with a list of miRNAs with the same binding site. Users could use some of these miRNAs as alternatives for the rerun of MREs design.
Figure 3: This window is resulted from the click on "View sequence and detail" button. The target site is colored organge.
Figure 4: This window the resulted from the click on "Design MREs" button. The mutated target site with low numbers of amino acid substitutions and modifications, higher binding score, and lower binding energy could be exported by users as an effective MRE for sequence mutation in wet-lab experiments.
Figure 5: This window is resulted from the click on "See other miRNAs that target the same binding site" button. Users could use some of these miRNAs as alternatives for the rerun of MREs design.
Figure 6: The search page for the miRNA-target site prediction by miranda for all human miRNAs and ORFs of seven RNA viruses. Users could explore the viral sequences and their target sites for a specific human-miRNA including design MREs for these target sites, as described above.

(1) A.J. Enright, B. John, U. Gaul, T. Tuschl, C. Sander, D.S. Marks; MicroRNA targets in Drosophila; Genome Biol. 2003; 5(1):R1. [Abstract]

(2) Perez et al. MicroRNA-mediated species-specific attenuation of influenza A virus. Nat Biotechnol. 2009 vol. 27 (6) pp. 572-6. [Abstract]

 

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    Last update: 24-Apr-2012    

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