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Generally in miRNA prediction most researchers do as Blast search with a set of miRNAs downloaded from miRBase with the parameters they require. Later on usually custom methods are utilized to get an area around the match area for structure prediction.

In one paper, I found that ~70 flanking nt of match area was taken as pre-miRNA for structural analysis while in this paper ~100 flanking nt of the match area was taken for pre-miRNA structure prediction. Any idea why so?

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up vote 1 down vote accepted

There is no hard and fast rule for how many nucleotides you have to select. If your miRNA is ~20nt and you take 70nt from both sides (average length of hairpins is ~84nt in humans), your total length will be 160nt. The point of taking $\pm70nt$ is that you don't know if your read is -3p or -5p. So take 70nt from both sides.

The maximum length of a human miRNA hairpin is 180nt for mir-3648 (90nt per half hairpin). In such cases you may take more flanking residues. But these cases are rare.

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