How to identify conserved and novel miRNA

Question

[khq5801]

I want to identify conserved and novel miRNA. I do not understand whether I need to align my NGS sample miRNA that has AGCT nucleotides with mature.fa file of miRBase that has AGCU using Bowtie, because I think the alignment of T and U will not be possible, or if I perform ncbi blastn with miRBase mature.fa file, then do I need to change the U in mature.fa file with T. How can I move forward, kindly provide your valuable suggestion.

[GenoMax]

I need to align my NGS sample miRNA that has AGCT nucleotides with mature.fa file of miRBase that has AGCU using Bowtie

That is correct. You will need to change the U's to T's if you download sequence from miRbase. You may want to use an established pipeline to do this. Here are some examples.

ENCODE project - https://www.encodeproject.org/microrna/microrna-seq/
SciLifeLab - https://github.com/SciLifeLab/NGI-smRNAseq
TCGA pipeline from BCGSC - https://github.com/bcgsc/mirna