How To Fetch The Coordinates For Different Domains In Mirna Precursor.

Question

[Lds]

Hi fellows,

Do you known how to fetch the coordinates for different domains in miRNA precursor, like the coordinates for stem, miR, miR*, loop or seed region.

Thanks in advance, I'm looking forward to your answers or suggestions.

Answer 1

[Leonor Palmeira]

This information is available in miRBase (see Stem-loop and Deep sequencing) but not readily available to download as such. What you can download is:

• all precursor miRNAs from miRBase in EMBL format, containing the annotation of mature miRNA positions here

One solution would be to run RNAfold on each precursor miRNA and extract the positions of the stem, loop.