Hai Stars, I want to identify known and conserved miRNAs from my data. For that i trimmed my reads (fastq Paired end) based on the length: 16bp minimum and maximum of 36 bp. For conserved miRNA identification i downloaded mirbase matured miRNA and i did homology search. But i didn't get any results because mirbase data base contains "U" base and which is not in my read.How to alignment when reference has "U" base instead of "T"
I recommend you Bowtie, but also, I recommend you map your reads against the entire genome and then count the read that maps to the known mirnas by using the gff3 of mirbase. If you map your reads to the fasta containing mirna sequences you will get biased results since there are some redundant miRNAs (mainly in mouse).