Single motif
  Composite motif
  Promoter fetcher



 Last Update:
  September 27, 2017


Compo is written in Python. It requires Python 2.5 installed, and the TAMO motif tools package (downloadable from the web).

Compo can be run from command line or in batch mode from command line (in the code directory). Details can be found in the sipped archives.

should be in fasta-format, should be in Transfac format. In batch mode, should be a folder containing subfolders for each data set. Each subfolder should then contain a sequence file and a PWM file. Example files are provided along with this readme-file.

Compo will by default run in parameter-free mode, where it estimates the best parameter values from a list of discrete possibilities. These lists are given in config.py and can be changed to contain different values, or to contain a single value if this is to be specified exactly.

Compo is freely available as Python source code in the following zip-file: Compo.zip

Predictions made by Compo on the benchmark data sets presented in the article: predictions.zip

For more information of the program contact Geir Kjetil Sandve by email: geirksa@ifi.uio.no

Bioinformatics & Gene Regulation
Department of Cancer Research and Molecular Medicine
Norwegian University of Science and Technology
Trondheim, Norway