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Old 09-22-2009, 01:08 PM   #1
sgombar
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Default Predicting Novel microRNA

Hello,

It is up to me to take nextgen sequencing data for my lab and come up with possible novel microRNA that might be within the data. I was wondering what people use as a prediction tool and why.

I want to be able to give a DNA sequence to a program and have it give me a probability value that a miRNA structure is contained within the sequence.

Thank you,
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Old 09-22-2009, 08:31 PM   #2
dina
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I once used RNAfold to check the possible folding and see if the structure is like a structure of miRNA. Then you can use miRANDA to seek for miRNAs predective targets.
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Old 09-24-2009, 12:16 PM   #3
sgombar
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Thanks for the info Dina. I have found a program mirDeep that wraps around RNAfold to do something similar to what I want but it is still more complicated than what I want. Ideally I want a program that I give a fasta file containing a sequence I think might have a precursor-miRNA and I want the program to just give me the probability of a precursor-miRNA. Do you know if anything like that exists?
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Old 09-28-2009, 10:10 PM   #4
Torst
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Quote:
Originally Posted by sgombar View Post
It is up to me to take nextgen sequencing data for my lab and come up with possible novel microRNA that might be within the data. I was wondering what people use as a prediction tool and why.
Is the sequencing data genomic DNA, or cDNA from a transcriptome?

If genomic DNA, you can try an RFAM search. If cDNA then you are probably in trouble as the next gen sequencing library would select out sequences of a certain size (eg. 250 bp for Illumina) and most of your miRNA would not be included.
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Old 01-01-2013, 08:02 AM   #5
edie1102
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Quote:
Originally Posted by dina View Post
I once used RNAfold to check the possible folding and see if the structure is like a structure of miRNA. Then you can use miRANDA to seek for miRNAs predective targets.
hi dina, I am using miRanda to find the miRNAs predective targets, and I get the preliminary results, but I don't know how to analyse the multiple restults, so, do you have some script for miranda or give me some advice? I will be grateful~~
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Old 01-20-2013, 10:38 PM   #6
jay2008
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hi sgombar,
miRdeep* may help you.
https://sourceforge.net/projects/mirdeepstar/
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