Our program in this website is based on the programs PriMir and Mirident, the softwares RNA-fold and Libsvm. You can download them using the links in this website.

Please also cite the appropriate methods paper for the analyses you have used.



PriMir: Shunmin He, Hua Su, Changning Liu, Geir Skogerbø, Housheng He, Dandan He, Xiaopeng Zhu, Tao Liu, Yi Zhao, Runsheng Chen (2008). "MicroRNA-encoding long non-coding RNAs." BMC Genomics 9:236.

    PriMir is a program to predict Pre-miRNA by score matrix based on eleven features found in the sequence or secondary structure of known pre-miRNAs.

    This program can be downloaded from here.



Mirident: Xiuqin Liu, Shunmin He, Geir Skogerbø, Fuzhou Gong, Runsheng Chen (2012). "Integrated sequence-structure motifs suffice to identify microRNA precursors". PLOS one 7:e32797.

    Mirident uses ss-motifs as features in a Support Vector Machine (SVM) algorithm for pre-miRNA identification.

    Mirident has its own website, you can visit its website to download it or download its program from here.


Rnafold

   The second-structure of pre-miRNA predicted by the webserver is identificatied by this software.

   You can download it included in the Vienna RNA Package in the website http://www.tbi.univie.ac.at/~ivo/RNA/


Libsvm

    A support vector machine (SVM) is used for classification and regression analysis. The standard SVM takes a set of input data and predicts, for each given input, which of two possible classes comprises the input, making the SVM a non-probabilistic binary linear classifier.

    You can download the SVM Software fit to you from the website http://www.svms.org/software.html.

    Libsvm can be downloaded from http://www.csie.ntu.edu.tw/~cjlin/libsvm/oldfiles/.

    The 2.86 version is used in our work and we recommend this version. http://www.csie.ntu.edu.tw/~cjlin/libsvm/

 


Publication

1.Shunmin He, Hua Su, Changning Liu, Geir Skogerbø, Housheng He, Dandan He, Xiaopeng Zhu, Tao Liu, Yi Zhao, Runsheng Chen (2008). "MicroRNA-encoding long non-coding RNAs." BMC Genomics 9:236.

2. Xiuqin Liu, Shunmin He, Geir Skogerbø, Fuzhou Gong, Runsheng Chen (2012). "Integrated sequence-structure motifs suffice to identify microRNA precursors". PLOS one 7:e32797.

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