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How to predict the mature miRNA from its precursor

Hello,

I am currently working on predicting ncRNAs using Infernal as my primary prediction tool. I have several datasets for different species containing microRNA precursors and their families, annotated based on Rfam. I am currently using RNAfold to predict the secondary structure and the MFE score to filter the results. However, to perform target prediction, I need to identify the mature miRNAs within the precursor sequences, and I am having difficulty finding suitable tools for this task. Can anyone provide me with some guidance on this matter?

rnafold microrna
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updated by colindaven colindaven • written by Beatriz • Beatriz

1 answer

Can you get mature miRNA fastq data from your species of interest, trim it multiple times to get the expected length, then map it ? I think bowtie1 was a decent mapper for miRNA data back then, there might be better tools now.

Have a look for public data using a tool like https://sra-explorer.info/

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written by colindaven colindaven

I am working with non-model species and do not have information on their mature miRNAs specifically. However, I am considering downloading all the possible mature miRNA sequences from mammals (my group of interest) that can be derived from the precursors I've found and mapping them. Would this be a viable approach?

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written by Beatriz • Beatriz

If there's any data from closely related species I would consider that too. miRNA mapping is very difficult, as genomes are large and miRNAs are tiny - 21 bp or similar. I'm sure you know this though.

Remember to go for exact matches and not allow mismatches in your mappings to avoid false positives, at least initially.

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written by colindaven colindaven

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