Search for possible miRNAs based on acquired transcript sequence

Question

[omer.k]

Hi, Very simple question. I have acquired a sequence which I think originates from a specific transcript. it is around 10kbp long. I'd like to use this sequence to find possible miRNAs which could potentially target it. What are my options? I'm open for suggestions using online platforms as well as stand-alone scripts (Win/Linux).

So far I've tried searching in many platforms, but seems like none have the option to search for miRNA based on user input sequence.

Thanks.

Answer 1

[Russ]

Do you have a list of known miRNAs for your organism (you can check mirbase)? If so, you can use any number of tools (e.g. miRanda, Targetscan - more can be found with a quick search)

[omer.k]

Hi Russ, For starters it'll be nice if I could use ALL homo sapiens known miRNA entries (any entry with 'hsa' prefix). Any idea as to where can such specific list be downloaded?

[Russ]

I don't know for sure if it's all of them, but here's a good start:

http://www.mirbase.org/cgi-bin/mirna_summary.pl?org=hsa

[omer.k]

Hmm, that may work. I've found that microRNA.org also provide "Good mirSVR score, Conserved miRNA" for Human (http://34.236.212.39/microrna/getDownloads.do).

Now that I have my list of possible miRNAs, what tools can I use to examine my sequence?

[Russ]

.... the ones I suggested in my answer. miRanda and Targetscan both allow you to scan your custom input sequence for the miRs you obtained from miRbase. There are other tools out there, too - up to you to decide which works best for you.

[biofalconch]

Are you using human transcripts? Just keep in mind that many of these microRNAs might target transcripts on specific species and change their targets greatly in another. That said, if that transcript is in ENSEMBL, you can go to TargetScan and check if your transcript has predicted target sites.

[omer.k]

Hey biofalconch, Yes, It is of human origin so indeed I am only interested in human miRNAs. As I've mentioned I am not interested in using an already existing entry from ENSEMBL, but use my own acquired sequence. E.g. paste my sequence and find potential miRNAs which could target it (put simply...)