doubt

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anjana
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Joined: 11/26/2013

hai,
i am new to the area of bioinformatics. i have been assigned to fold the 200 bases + miRNA +200 bases (total some 425 bases) using mfold - rna fold. i folded the sequence with default parameters. is the delta g displayed the minimal free folding energy? how do i select the mirna precursor from the data? can u plz help me out.

zukerm
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Joined: 11/12/2010
miRNA precursors in some

miRNA precursors in some organisms can be very long and difficult to detect. This is true, for example, in Arabidopsis thaliana. I am assuming that you are looking for human, mouse or similar miRNA precursors.

If this is the case, the pre-miRNA is about 100 bases in length and folds into a long stem-loop structure. There should be no branching, or perhaps some minor branching. Examine the energy dot plot. The precursor should stand out in the plot. Look for a stem of length 50 (roughly) with a few mismatches and bulges. See, for example, Figure 1 in an article by J. Krol et al.:  
Structural Features of MicroRNA (miRNA) Precursors and Their Relevance to miRNA Biogenesis and Small Interfering RNA/Short Hairpin RNA Design.