Question: miRNA structure file (hairpin structure) from precursor miRNA sequences
0
gravatar for vkgaur25
6 weeks ago by
vkgaur2530
vkgaur2530 wrote:

Hi, Probably this is a bit outside of the kinds of questions asked here but I am unable to find any suitable answer of my question so asking here. I have RNA-Seq data and I am looking for isomiRs . For alignment step I need a hairpin fasta file and a structure file (Mirna.str) . I know both of these are available at miRBase but here's the catch. I have my own lab produced annotation table for miRNA (i.e. I have fasta file for precursor miRNA) but I want to build structure files (.str) based on my miRNA database.

For example for -hsa-mir-192 structure would look like this (this is from miRBase)

enter image description here https://postimg.cc/image/652mmlxa5/

Does anyone know any tool or way to do this?

rna-seq • 118 views
ADD COMMENTlink modified 6 weeks ago by toralmanvar510 • written 6 weeks ago by vkgaur2530
2

You can have a look on Mfold

ADD REPLYlink written 6 weeks ago by nitinnarwade1504200
2
gravatar for toralmanvar
6 weeks ago by
toralmanvar510
toralmanvar510 wrote:

You can also use RNAfold web server or standalone RNAfold program from ViennaRNA package for getting precursor structure.

ADD COMMENTlink written 6 weeks ago by toralmanvar510
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