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Looking for tool that searches a list of genes for common MiRs

MiR MicroRNA

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#1 LSJUMDPHD

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Posted 26 September 2012 - 09:52 AM

Hi Guys,

First time poster in the house. Good to have this resource.

Question: Is there a tool that will allow me to enter a list of genes and "blast" them to see if they share predicted MiRs?? I have a list of 200 genes and I'd rather not have to look up their predicted MiRs individually.

Looking forward to hearing back and to contributing in the future.

#2 pcrman

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Posted 26 September 2012 - 03:18 PM

I don't think there are existing online tools allowing you to do that. This would need you to run some programs on your computer and parse the results. It should be a simple task for a bioinformatics guy. What you need to do is to first retrieve the 3'utr of the 200 genes from database (for example you can biomart), and all miR sequences, then run some kind of prediction program (e.g. miRanda), then examine the result to see the commonly shared miRNAs. To do this, a custom script is needed.




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