Computational Regulatory Genomics

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Pipeline for the Identification of Plant miRNAs


We developed the PIPmiR algorithm to identify novel plant miRNA genes from a combination of deep sequencing data and genomic features.

The algorithm can be used as the full pipeline, as just a classifier, or as just a plant precursor sequence predictor

The executibles for PIPmiR v1.1 can be downloaded here. (View the README file)
Note: PIPmiR is provided for academic use only, if you wish to use it in another setting please contact Uwe Ohler.
Update (v1.1)
I have now included the ability to generate and specify your own classifier training file.

The algorithm was initially developed as a series of perl scripts The JAVA implementation mentioned above has been tested and is much easier to use. However, if you find a bug, please don't hesitate to contact us.

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