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-   -   novel plany miRNA prediction without reference (http://seqanswers.com/forums/showthread.php?t=11507)

Giorgio C 05-20-2011 06:58 AM

novel plany miRNA prediction without reference
 
Hy, we made a 454 run of a miRNA library of a non sequenced plant. What pipeline you would suggest to predict novel miRNA considering that we have not any reference ?

Thank you very much

NicoBxl 05-22-2011 11:50 PM

You can use the genome of a very related plant.

Otherwise I don't know how to do such prediction without a reference genome..

rwenang 05-23-2011 01:08 AM

There are some tools which predict the precursor mirna structure from the sequence. If im not mistaken they used HMM to do that, but I cannot remember the name of the tool.

Giorgio C 05-23-2011 02:25 AM

Thank you very much. I am in diffuculty about this, i'll try different ways.


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