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microRNA alignment - (Mar/14/2005 )


I am trying to identify a micro RNA that targets our gene of interest. I'm finding it hard to determine whether the micros that i have cloned are specific to our region due to a lack of sequence alignment programmes that allow for the mismatches and gaps that occur between micro RNAs and their targets.

Basically....what is a good programme to align micro RNAs with potential targets?



I found the program miRanda is the best one. It needs local installation.




Could anyone tell me how to install and use miRanda software?
I am using Windows XP computer, and had installed J2SE 5.0. But when opening miRanda v1.0b, the program says error, although MiRanda Java Interface v1.0 window opens. Further I have no idea how to use it. Does this software already have miRNA library, or should I make it like mouse miRNAs, human RNAs...?

Thank you for your help.

Tomo sad.gif


If the java interface doesn't work, try the command line version. You just launch a command window by going to start->run and type cmd, then go to the folder where mirnada resides. Before you run the program you have to create two FASTA files one holding your miRNA, the other holding the sequences to be scanned. Then type miranda mirna_file sequence_file output_file. There is a detailed instruction coming with the download.

You have to download miRNA library from


Thank you very much, pcrman.
It's working now.


QUOTE (Tomo @ Mar 28 2005, 06:06 PM)
Thank you very much, pcrman.
It's working now.

My project sounds similar to yours becholmes. I've been using miranda on a 2.6 linux kernel for a few months, I want something to verify my results. Looking at the source code, it is clear how they are aligning - but I have to wonder what others are doing.
Has anyone found alternative tools for prediction alignment?
Thank you much smile.gif