PolyA_SVM: analysis and prediction of mRNA polyadenylation sites by Support Vector Machine

Current version: 2.2 (Click here to the web server)

INTRODUCTION:

This program takes a file containing DNA/RNA sequences in the FASTA format as input, and 1) makes prediction for putative mRNA polyadenylation sites [or poly(A) sites] and/or 2) generates results indicating the occurrences of different cis-elements. The program is implemented in PERL and runs under UNIX/LINUX systems. It requires the LIBSVM library (also included in the package).

DOWNLOAD & INSTALLATION:

1. Click here to download the current version of PolyA_SVM to a directory, e.g. /home/polya_svm/.
2. Extract the tar file to the directory by typing tar -zxvf polya_svm_x.x.tar.gz 
3. A directory named "polya_svm_x.x" will appear. Switch to it by typing cd polya_svm_x.x 
4. Type polya_svm.pl to learn how to use the program. 

PREVIOUS VERSIONS:

  • PolyA_SVM_1.0: polya_svm_1.0.tar
  • PolyA_SVM_1.1: polya_svm_1.1.tar
  • PolyA_SVM_1.1 (MS Windows): polya_svm.1.1.windows.zip
  • REFERENCES:

  • Cheng, Y., Miura, R.M., and Tian, B. (2006). Prediction of mRNA polyadenylation sites by support vector machine. Bioinformatics 22:2320-5.
  • Hu, J., Lutz, C.S., Wilusz, J., and Tian, B. (2005). Bioinformatic identification of candidate cis-regulatory elements involved in human mRNA polyadenylation. RNA 11: 1485-1493.
  • Chang, C.-C. and Lin, C.-J. (2005) LIBSVM: a Library for Support Vector Machines (www.csie.ntu.edu.tw/~cjlin/libsvm).
  • CONTACT:

    Please contact Bin Tian (btian@umdnj.edu) for questions/comments/suggestions.

    Last updated: 9/16/2008
    Tian Lab, UMDNJ-New Jersey Medical School