M.W. Mak, J. Guo, and S.Y. Kung, "PairProSVM: Protein Subcellular Localization Based on Local Pairwise Profile Alignment and SVM", IEEE/ACM Trans. on Computational Biology and Bioinformatics, to appear.
　

Resources for download:

• Paper
  　

• The sequences of Huang and Li's dataset in Matlab format
  　

• The profiles (PSSM and PSFM) of Huang and Li's dataset in Matlab format
  　

• The PairSeqSVM scoring matrix
  　

• The PairProSVM scoring matrix 
  　

• Matlab programs
  Note  1: Contact Man-Wai Mak for the profile alignment functions "profile_align.m" and
                profile_align_mem.m"         
            2: You need Matlab 7 Bioinformatics Toolbox to run sequence alignment.

• Appendix:

  A) Profile Alignment Algorithm

  B) Architecture of the Prediction System

  C) Redundancy-Removed Dataset

  D) Definition of MCC

  　

• Presentation in MLSP'06

   

To run the five-fold cross validation, you also need to download the Matlab machine learning toolbox Spider.

If you have any question, please contact Dr. Man-Wai Mak or Jian Guo.

M.W. Mak's Homepage

http://www.eie.polyu.edu.hk/~mwmak/mypage.htm