Title: De Novo SVM Classification of Precursor MicroRNAs from Genomic Pseudo Hairpins Using Global and Intrinsic Folding Measures

Supplementary materials:

  1. PDF (566 Kbytes)
  2. Datasets (13 Mbytes; Features (tab-limited) and results (tab-limited) of precursor miRNAs, ncRNAs, mRNAs, and pseudo hairpins).
  3. Results (59 Mbytes; Results (tab-limited) of precursor miRNAs, ncRNAs, mRNAs, and pseudo hairpins).

Computational pipeline requirements:
Please ensure the following software are installed before proceeding:

  1. Linux-based system or Cygwin
  2. Perl 5.8.3 (at least)
  3. GNU GCC 3.0 (at least)
  4. 50 to 100 MB (at least)
  5. Source codes for libsvm (Version 2.82). Original link is at http://www.csie.ntu.edu.tw/~cjlin/libsvm/
  6. Executable of Naive and Full Bayes Classifier Induction (Version 2.14) for running on Linux-based system x86 32-bit Pentium. Original link is at http://fuzzy.cs.uni-magdeburg.de/~borgelt/bayes.html if the c source codes is required.
  7. Executable of Table Utilities for running on Linux-based system x86 32-bit Pentium. Original link is at http://fuzzy.cs.uni-magdeburg.de/~borgelt/table.html if the c source codes is required.
  8. Perl module source codes for Statistics::ROC (Version 0.01). Original link is at http://search.cpan.org/~hakestler/Statistics-ROC-0.01/ROC.pm
  9. Perl module source codes for Statistics-Descriptive (Version 2.6). Original link is at http://search.cpan.org/~colink/Statistics-Descriptive-2.6/Descriptive.pm
Please download the following scripts, executable, and datasets:
  1. Install.bash
  2. Datasets. Values of features extracted from precursor miRNAs, ncRNAs, mRNAs, and pseudo hairpins.
  3. Scripts. They glue the different software together.
To replicate all the results in the publication:
Run "./Install.bash".
  1. It creates a directory MIPRED2006
  2. Decompress datasets
  3. Decompress scripts
  4. Train and test the 3SVM, bayes, miPred classifier models. In order to extract the features, please see BIOINFO 06-004 for details.
Their use is free purely for non-profit and academic purpose adhering to the GNU General Public License (GPL).

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