May 19, 2009
36 MB
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Files from Simmons et al
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Files cited in Simmons et al
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
SAFA for Mac OSX Standalone
Standalone Application for Macintosh OS X 10.4 (Tiger)
v11b
Apr 23, 2007
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
Standalone for Microsoft Windows XP
v11b
Apr 23, 2007
Documentation Links
Dec 19, 2007
SAFA Quicktime Video Tutorial
Apr 23, 2007
Documentation
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
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
Apr 23, 2007
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
A series of input and output files for testing SAFA
v11b
Apr 23, 2007
Download Links
Apr 23, 2007
3 MB
Any
Data/images/video
Example Gel File used in Documentation
Apr 23, 2007
16 MB
Any
Data/images/video
Example Matlab Dump File post quantification
Apr 23, 2007
398
Any
Data/images/video
Example Sequence File (in FASTA format)
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)