Predicting Novel microRNA

[sgombar]

Hello,

It is up to me to take nextgen sequencing data for my lab and come up with possible novel microRNA that might be within the data. I was wondering what people use as a prediction tool and why.

I want to be able to give a DNA sequence to a program and have it give me a probability value that a miRNA structure is contained within the sequence.

Thank you,

[dina]

I once used RNAfold to check the possible folding and see if the structure is like a structure of miRNA. Then you can use miRANDA to seek for miRNAs predective targets.

[sgombar]

Thanks for the info Dina. I have found a program mirDeep that wraps around RNAfold to do something similar to what I want but it is still more complicated than what I want. Ideally I want a program that I give a fasta file containing a sequence I think might have a precursor-miRNA and I want the program to just give me the probability of a precursor-miRNA. Do you know if anything like that exists?

[Torst]

It is up to me to take nextgen sequencing data for my lab and come up with possible novel microRNA that might be within the data. I was wondering what people use as a prediction tool and why.

Is the sequencing data genomic DNA, or cDNA from a transcriptome?

If genomic DNA, you can try an RFAM search. If cDNA then you are probably in trouble as the next gen sequencing library would select out sequences of a certain size (eg. 250 bp for Illumina) and most of your miRNA would not be included.

[edie1102]

I once used RNAfold to check the possible folding and see if the structure is like a structure of miRNA. Then you can use miRANDA to seek for miRNAs predective targets.

hi dina, I am using miRanda to find the miRNAs predective targets, and I get the preliminary results, but I don't know how to analyse the multiple restults, so, do you have some script for miranda or give me some advice? I will be grateful~~

[jay2008]

hi sgombar,
miRdeep* may help you.

https://sourceforge.net/projects/mirdeepstar/