cant find a relevant mirna predictor

Question

[micro32uvas]

Hi i am quratulain

I am working on mirna . i have a complete list of it now but i am finding it bit difficult to find the appropriate mirna predictor in animals(cow). I am gone through dozens of them by now but cant figure out.

All i want is to submit my query hairpin file and get results whether how many of those sequences are able to be mirna.

P.s. i am a beginner!

[Michael]

What do you want to predict/detect?

• miRNA de-novo from genome sequence?
• miRNA from miRNA sequencing?
• miRNA targets from miRNA sequences?

Please clarify.

[micro32uvas]

its miRNA denovo from genome sequence.

[Michael]

Mind a lot of false positives in this case.

[micro32uvas]

Dear andrew.j.skelton73, I have tried mirdeep2 but thats not get my desired results.

Answer 1

[andrew.j.skelton73]

Try out miRDeep2

[Michael]

In my understanding miRDeep requires miRNA sequencing data as input, do have a different protocol?

[andrew.j.skelton73]

Ah whoops, that's my bad, good catch. I thought I read that OP did miRNA sequencing, not WGS!

[micro32uvas]

yeah, it must include a lot of false positives and I actually want to rule them out. I have mirna sequencing data with me. I can't find one, which takes a list of mirna sequences as an output and rule out which doesnt form hairpin or typical mirna structure

[andrew.j.skelton73]

Well if you have miRNA sequencing, miRDeep2 is the tool you want, if you have WGS, then I'm not sure what you can do really, other than aligning it to your reference sequence, and looking for differential expression of known miRNA genes.