Jump to content

  • Log in with Facebook Log in with Twitter Log in with Windows Live Log In with Google      Sign In   
  • Create Account

Submit your paper to J Biol Methods today!
Photo

program for microRNA (miRNA) target prediction


  • Please log in to reply
7 replies to this topic

#1 becholmes

becholmes

    member

  • Members
  • Pip
  • 2 posts
0
Neutral

Posted 14 March 2005 - 05:53 PM

Hello

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?

Thanks

#2 mario2004

mario2004

    member

  • Active Members
  • Pip
  • 24 posts
0
Neutral

Posted 14 March 2005 - 06:07 PM

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

miRanda is an algorithm for finding genomic targets for microRNAs. This algorithm has been written in C and is available as an open-source method under the GPL. MiRanda was developed at the Computational Biology Center of Memorial Sloan-Kettering Cancer Center.

http://cbio.mskcc.or...iranda_new.html

The windows version: http://cbio.mskcc.or...3/src/jmiranda/
The Mac version: http://cbio.mskcc.or...3/src/binaries/
The Windows Cygwin version http://cbio.mskcc.or...3/src/binaries/

The latest command line (linux or unix) version http://www.microrna....getDownloads.do

Mario

#3 Tomo

Tomo

    member

  • Members
  • Pip
  • 4 posts
0
Neutral

Posted 25 March 2005 - 04:41 AM

Hello,

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 <_<

#4 pcrman

pcrman

    Epigenetist

  • Global Moderators
  • PipPipPipPipPipPipPipPipPipPip
  • 1,165 posts
67
Excellent

Posted 25 March 2005 - 11:39 AM

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 http://www.sanger.ac...mirna/browse.pl

#5 Tomo

Tomo

    member

  • Members
  • Pip
  • 4 posts
0
Neutral

Posted 28 March 2005 - 05:06 PM

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

#6 saadianaseem

saadianaseem

    member

  • Members
  • Pip
  • 1 posts
0
Neutral

Posted 25 September 2012 - 10:02 PM

I am having linux installed on my system and trying to download MiRanda as directed on mirna.org but not possible to download, plz help.

#7 vitalgene

vitalgene

    Enthusiast

  • Active Members
  • PipPipPipPipPip
  • 53 posts
0
Neutral

Posted 26 September 2012 - 11:59 AM

i like this guy-
http://www.microrna..../getGeneForm.do

#8 miR_fan

miR_fan

    member

  • Members
  • Pip
  • 3 posts
0
Neutral

Posted 05 June 2013 - 10:06 PM

Hello everyone...

This is is continuation with the miRNA target perdiction. I am trying to find out human miRNA target on a virus gene of interest. Can anyone suggest some tool/software to do the required..

Thanks in advance




Home - About - Terms of Service - Privacy - Contact Us

©1999-2013 Protocol Online, All rights reserved.