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Old 05-20-2011, 07:58 AM   #1
Giorgio C
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Default 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
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Old 05-23-2011, 12:50 AM   #2
NicoBxl
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You can use the genome of a very related plant.

Otherwise I don't know how to do such prediction without a reference genome..
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Old 05-23-2011, 02:08 AM   #3
rwenang
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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.
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Old 05-23-2011, 03:25 AM   #4
Giorgio C
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Thank you very much. I am in diffuculty about this, i'll try different ways.
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