SAFA Footprinting Software
Downloads
Files cited in Simmons et al  Monitor Package
In this folder are files cited in the Simmons et al. paper. Please read the "Read Me Text for Folders" text for further description of the files in the folder.
Files from Simmons et al
May 19, 2009

Download Links

Name File Type Platform Updated
simtk file 2.zip (38422 kB) -- Any May 19, 2009
Description: Files from Simmons et al

SAFA for Mac OSX Standalone  Monitor Package
Standalone Application for Macintosh OS X 10.4 (Tiger)
v11b
April 23, 2007
Notes

Download Links

Name File Type Platform Updated
SAFA_MACv11b.zip (73592 kB) binary Mac Apr 23, 2007
Description: Mac Standalone (Tiger, 10.4)

Documentation Links

SAFAUserGuide_v1_1.pdf (1366 kB) Apr 23, 2007
Description:
SAFA_Video_tutorial-.zip (99498 kB) Dec 18, 2007
Description: SAFA Quicktime Video Tutorial

    Please cite these papers
  • 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. (2005)

SAFA for Windows Standalone  Monitor Package
Standalone for Microsoft Windows XP
v11b
April 23, 2007

Download Links

Name File Type Platform Updated
SAFA_WINv11b.zip (104883 kB) binary Windows Apr 23, 2007
Description: v11b

Documentation Links

SAFAUserGuide_v1_1m.pdf (1366 kB) Apr 23, 2007
Description: Documentation
SAFA_Video_tutorial_.zip (99498 kB) Dec 18, 2007
Description: SAFA Quicktime Video Tutorial

    Please cite these papers
  • 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. (2005)

SAFA Source Code  Monitor Package
This is the SAFA Source Code that requires Matlab. If you own a copy of Matlab, you should download this instead of the Standalones as the performance is better.
v11b
April 23, 2007
Notes

Download Links

Name File Type Platform Updated
SAFAv11.zip (345 kB) code Any Apr 23, 2007
Description:

Documentation Links

SAFAUserGuide_v1_1s.pdf (1366 kB) Apr 23, 2007
Description:

    Please cite these papers
  • 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. (2005)

SAFA v11 Example Files  Monitor Package
A series of input and output files for testing SAFA
v11b
April 23, 2007

Download Links

Name File Type Platform Updated
example.gel (3988 kB) data Any Apr 23, 2007
Description: Example Gel File used in Documentation
p4p6gel_PostQuantify.mat (17649 kB) data Any Apr 23, 2007
Description: Example Matlab Dump File post quantification
TtLSU.fas (1 kB) data Any Apr 23, 2007
Description: Example Sequence File (in FASTA format)

Documentation Links

SAFA_Video_tutorial.zip (99498 kB) Dec 18, 2007
Description: Video Tutorial For SAFA Usage in Quicktime

    Please cite these papers
  • 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. (2005)