1- Download the archive file

   Please download the archive files of Predyflexy 1.3 : predyflexy1.3.tar.gz.
Please notice the tools only are dedicated to be use with a Linux OS (mainly Ubuntu).

2- Install

   type "tar -xzvf predyflexy1.3.tar.gz" in the proper directory.

   it will create three directory : "DATA", "SOFTS", "src"
   with three files "pred.py", "README.txt", "install.txt"

3- External tools

   4 other external tools are needed to perform the flexibility prediction.

      a- blast-2.2.09 with the dedicated databank (swissprot 2006).
      b- svm_classify from SVM-light V6.01.
      c- svm-scale from libsvm 2.81.
      d- get_clean_matrix.

   Two VERY important points: (i) the version of BLAST is critical (as the use of the proper databank). Indeed, we have optimized the SVMs with PSSMs coming with the default parameters of this version. PSSMs are highly sensitive to the last improvements of BLAST, i.e., they are very different with recent BLASTs, they give so poor prediction scores. (ii) the last three tools are supposed to be in subdirectory SOFTS/, but they can be install somwhere else (proper options must be given, see next sections). SVM-light and libsvm versions are supposed to be less critical than the BLAST version. Tests with other versions have given equivalent results.

   In case you do not find on the web the proper versions of the tools, see subdirectory download/external_src/, or in an unique zip file external_src.zip.