Extract pre-mirna using sliding window.

Question

[bioinfo223]

Hello,

I want to extract the precursor of miRNA, and for this, I need to follow this step.

precursor sequences by taking a sliding window of about 100 nt (moving in increments of approximately 10 nt) from the region ~80 nt upstream of the beginning of the mature miRNA to ~80 nt downstream of the miRNA.

Please let me know how can i do this step. Should I use bedtools for this? I am confused kindly let me know.

[mohammadhassanj]

For known ones you can use miRbase

Here is an article related to the discovery of novel miRNAs