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Old 02-17-2010, 01:46 PM   #1
PRJ
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Default miRNA identification in plants using smallRNA deep SEQ data

I am trying to identify miRNAs (novel and conserved) in a plant species using small RNA deep sequencing and a draft genome (~8x coverage). The only problem is that we are not able to release the genome publicly yet. I have seen that there are online programs that have published genomes uploaded - miRcat, miRanalyzer, etc.

I would like to run a program on my computer to identify miRNAs based on sRNA SEQ and a draft genome. I know there is miRDeep but this seems to be specifically for animal miRNAs which have a more constrained hairpin structure.

Does anyone know of any programs that I could run on my own computer, not on the internet, to identify miRNAs using my sRNA SEQ and draft genome?

Does anybody have any other ideas? - Thanks
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Old 09-13-2013, 03:14 AM   #2
Latifa77
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Hi,
How did you solve your problem? Does anyone who is working with miRNAs in plant and deep sequencing ??? Please.
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Old 09-13-2013, 03:31 AM   #3
Blahah404
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The seqmentSeq R package is designed for small RNA discovery in plants.

Paper is here: http://bioinformatics.oxfordjournals...28/4/457.short
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Old 09-13-2013, 03:54 AM   #4
Latifa77
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Hi Blahah404,
Thanks for you answer. I see that seqmentSeqR is for siRNAs, but I woukd like a program to identify miRNAs.
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Old 09-13-2013, 04:11 AM   #5
Blahah404
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Whoops, sorry, misread the question.

Two options that I know of:

mirDeep-P
ShortStack
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