Quick Install Guide: 1) Install Python 2.2+ from http://www.python.org 2) Install Biopython.org from http://www/biopython.org 3) Download and compile the savgol module in TISEAN, http://lists.mpipks-dresden.mpg.de/~tisean/TISEAN_2.1/index.html - just compile the full package and copy the module from TISEAN-2.1/source_c/sav_gol to the DisEMBL directory. 4) Compile disembl's neural network (gcc -O3 disembl.c -o disembl) 5) Set correct paths to the neural net binary and savgol at the top of the script: from /PATH/DisEMBL-1.x to the correct path Now you should be able to parse in a sequence file containing multiple fasta entries... just do a "./DisEMBL.py 8 8 4 1.2 1.4 1.2 sequence_file" if you want to save the results add " > resultfile.disembl" after the command