User:TheLarry/Notebook/Larrys Notebook/2009/07/01

From OpenWetWare
Jump to navigationJump to search
Owwnotebook icon.png Project name Report.pngMain project page
Resultset previous.pngPrevious entry      Next entryResultset next.png

Back to SDM

It is time for me to implement cross correlation into the comparing shit i do. and all that jazz.

Note: Koch wants to add a shift [Cross Correlation] and a stretch [unknown but koch said a multiplying factor may do this. i'll work on it after cross correlating].

Using primarily three pages from wang lab to see me through it.

  1. Shundrovsky 2006 "Probing SWI/SNF remodeling of the nucleosome by unzipping single DNA molecules"
  2. Deufel 2006 "Detection of Forces and Displacements along the axial direction in an optical trap"
  3. Hall 2009 "High-resolution dynamic mapping of histone-DNA interactions in a nucleosome"

Cross correlation looks easy. I just gotta write a .vi to run this formula.

The Hall paper mentions a way they compare graphs from Orear "NOTES ON STATISTICS FOR PHYSICISTS, REVISED." When I am done with this; this paper may be worth looking through to improve my match score.

OK i wrote my first cross correlating .vi

Here is a cross correlation between theoretical pBR322 and experimental 322. This is the best data we have. The theory came from the file in Chrom 12 folder, and the experimental came from the file in Chrom 17
Here is the equation I used. It came out of Shundrovsky 2006 mentioned above. It was in the supplemental part.