micro RNA traget prediction - (Jan/16/2006 )

Hi,

I would like to know whether there is any target for any micro RNA on my sequence of interest. Is there any web-program for that? Or, is there anybody to help me? Sanger centre's site I visited, but, it wouldn't allow to upload sequence.

I appreciate your help.

Thanks,

utpal

What is your sequence of interest ... you can look in miRBase (Sanger centre's site ... or use the software "miranda" ... I can donwload sequence of miRBase in Browser ... I'd selectioned the specie of my interest and fine ... In this DB you can get any sequence and download ... bye..

Thanks for your response.

I tried both of the sites. As far as I understand, they don't allow me to upload the sequence. I have to search with the gene name. The problem is, for whatever reasons, the 5'UTR of my gene of interest is missing in the genebank or ensembl database. It is known and I have the 5'UTR.

The trouble is, if I ask these programs to find microRNA targets, it simply doesn't search over there. But, this is my experience. I am new in this field. So, I might be doing something wrong. However, if, you have some suggestions, please let me know.

Thanks.

Hi,

There are two ways of finding potential miRNA targets on your sequence.

1. Use online miRNA target prediction tools such as the one on Sanger website which does provide search by sequence. You have to scroll down to the sequence input box to paste your sequence there.
2. Download the miRanda program onto your computer, download all miRNA sequence (only hundreds) as fasta file, and prepare your only gene sequence as fasta file too. Run the program. This gives you much control over many parameter settings.

Great help.

I tried option 2 and it worked.

Thanks.

Hi¡¡ I have several doubts:

1.- How can I get a windows version of miRanda?

2.- Is it the best program for target prediction?

3.- What do you opine about other softwares like microInspector?

4.- When I upload my UTR sequence, I obtein many hits, most of them with a score >150. However, when I analyze these hits, I see there isn´t perfet matching in the seven nucleotides more 5´. Do you think it might be worthwhile to try validate these results?


lots of thanks

Sorry for my English