ShapeFinder

What is ShapeFinder?

It's a tool for processing trace data for analysis of SHAPE data. It was written primarily by Morgan Giddings and Jessica Severin at the University of Wisconsin-Madison, in Lloyd Smith's lab and was known as BaseFinder at that time. The program was started in 1991 by Morgan, and continued refinement through 1997.

How to Install?

Prior to installation, it is best to manually delete the previously installed BaseFinder and/or ShapeFinder. Next, Drag and Drop the ShapeFinder.app file into the Applications folder.

How to Build?

You'll need to download the source code from the BaseFinder repository. Open the file BaseFinder/BaseFinder.xcodeproj in Xcode. Select the ShapeFinder Target and build. The BaseFinder project is set up to build as a universal binary and supports Mac OS X 10.4 and 10.5. Have fun!

Other contributors:

Mike Koehrsen
Suzy (Vasa) Stiegelmeyer
Nicolas Guex

Citation

Giddings MC, Severin J, Westphall M, Wu J and Smith LM, "A Software System for Data Analysis in Automated DNA Sequencing", Genome Research, 1998, 8:644-665

Vasa SM, Guex N, Wilkinson KA, Weeks KM and Giddings MC, "ShapeFinder: A software system for high-throughput analysis of RNA structure", RNA, 2008, 14(10):1979-1990.

ShapeFinder Release Notes

Version 0.2

-GUI issue with Leopard (10.5) items in lists, such as Script Inspector, etc. were not highlighting when selected.
-Removed Deconvolution Tool and Filter FFT tools from the list of tools
-Added Mobility Cubic tool to the list of tools

Version 0.1

-Birth of ShapeFinder name. Based on BaseFinder version 6.2.10

Known bugs/issues

- BaseFinder cannot save in ESD format. So, the first time the user tries to save an ESD file after opening, the save panel will come up, requiring the choice of a new format.

drsuuzzz/ShapeFinder