discovering micrornas from deep sequencing data using...
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Discovering microRNAs from deep sequencing data using miRDeep
Lin Min
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miRNA
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1. Map to genome and discard reads • Map to many loci • Map to rRNA tRNA
Flow Chart
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2. Excise sequence from genome using not discarded reads
Flow Chart
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3. Predict secondary structure and discard unlikely ones
Flow Chart
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Core algorithm
Flow Chart
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Features: • Reads signature
Core Algorithm
Find features to distinguish miRNA from noise
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Features: • Reads signature • Structural stability
Core Algorithm
Find features to distinguish miRNA from noise
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Core algorithm
Features: • Reads signature • Structural stability • 3’ end overhang
Core Algorithm
Find features to distinguish miRNA from noise
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Features: • Reads signature • Structural stability • 3’ end overhang • 5’ end conservation
Core Algorithm
Find features to distinguish miRNA from noise
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Core algorithm
Features: • Reads signature • Structural stability • 3’ end overhang • 5’ end conservation
Pre/bgr
Naïve Bayesian Model
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C. elegans.
116 Passed Cut off 103 previously known 13 new
5 are verified by northern 4 out of them are detected
Results
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Human
173 Passed Cut off 163 previously known (28%) 10 new
Results
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206 Passed Cut off 3 previously known 203 new
Dog
Results
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Thank you