miRNA are a class of post translation regulators. They are short ~22 nucleotide RNA sequences that bind to complementary sequences in the 3’ UTR of multiple target mRNAs, usually resulting in their silencing.
targetScan and lot of them. you want to predict the target of one or more miR?
Hi Girish... I agree about the target integration tools. It is nice to use an application that will run several prediction algorithms and compare them. I will recomend you Mirwalk and Mirecords... You can find them in my compilation of tools miRNAtools...
http://sites.google.com/site/mirnatools
Actually I want to predict miRNA target in human, plant, bacteria, & fungi. After prediction I want to check similarity between them so which tool should I use?
Where should I get Important speciality of specific tools.......?
Please help me....
Hi Girish,
You can use miRWalk database (mirwalk.uni-hd.de) for possible miRNA targets in human. Additionally, a comparative analysis of targets resulting from 10 different prediction data sets can be conducted using miRWalk.
Concerning similarity,
First step is to produce an aligned profile of UTR , mRNA, or promoter of mentioned species. You can interrogate Ensembl and/or UCSC database to produce such alignment file(s).
Second step is to download the TargetScan or miRanda and run them locally to produce possible conserved/non-conserved targets. More information on input file formats can be found here (http://www.targetscan.org/cgi-bin/targetscan/data_download.cgi?db=vert_61).
Hope this helps!
Best wishes,
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