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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

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May 19, 2009
36 mB
Any
Other
Files from Simmons et al


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SAFA for Mac OSX Standalone
Standalone Application for Macintosh OS X 10.4 (Tiger)
v11b
Apr 23, 2007

Notes

Download Links

Apr 23, 2007
70 mB
Mac OS X
Application/binary
Mac Standalone (Tiger, 10.4)

Documentation Links

Apr 23, 2007

Dec 19, 2007
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)


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SAFA for Windows Standalone
Standalone for Microsoft Windows XP
v11b
Apr 23, 2007

Download Links

Apr 23, 2007
100 mB
Windows
Application/binary
v11b

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)


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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

Notes

Download Links

Apr 23, 2007
336 kB
Any
Source code

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)


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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)

Documentation Links

Dec 19, 2007
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)


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