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SAFA

Semi-Automated Footprinting Analysis Alain Laederach, Rhiju Das, Sam Pearlman, Dan Herschlag, Russ Altman (C) Stanford University, 2004
Ported to a new GitHub repository for modernization by R. Das, Stanford University.

Getting Started

  • Install MATLAB 2014 or later.
  • In MATLAB, find the menu item "Environment/ Set Path..." and add the the directory SAFA/src.
  • Check out the example files in SAFA/example
  • Better docs are needed -- for now, check out User Guide at SAFAUserGuide_v1_1s.pdf, which will be updated pretty soon.
  • In the meanwhile, if you have advice for other SAFA users or questions, contact us at [email protected].

Reference

Das, R., Laederach, A., Pearlman, S.M., Herschlag, D., Altman, R.B. (2005) "SAFA: Semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments", RNA 11:344-354 Link