Hi everyone,

I've been having a longstanding issue with the miRNA binding tools and doing the alignments on the NEEDLE aligner (don't ask). I feel like I'm missing something.

For example if i were using RNA22 you have to input the mirna sequence (the example they provide has Ts while mirbase outputs the mature sequence with the appropriate Us). Therefore I just changed my U with T for my miRNAs.

The example that is included for the transcript also has Ts, which is the same as what you get in the trainscript ensembl sequences.

So if i wanted to find binding sites in the 3' UTR regions I would have to take the sequence and perform a reverse complement before searching for heteroduplexes at the "mRNA" level as the miRNA would pair to the "RNA" sequence A-Ts?

If i was doing alignemnts using needle aligner i am searching for actual alignments A-A etc.

I would input the mirna sequence with U converted to Ts, and the normal 3 UTR sequence??

Am I getting this right, someone please explain..

Thank you