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==September 2== *'''TO DO:''' **Add in GC content, AT content for arms and target region for ''effects'' plots. **Make slides; show each factor's effect graphs with explanation and a comparison of Proximal/Distal Bases (including Dr. Li's data) ***Describe how these curves will be used to affect scoring in next set of probes ***Take how score is currently calculated into account, suggest modifications? ***Decide how best to scale everything. *'''PowerPoint''' **Analyzed data and made preliminary powerpoint of results. **Found that: ***1) For the proximal ligation character, G is preferred, followed by C, A, and then T. ***2) A high Tm for the ligation arm is good. ***3) A low Tm for the extension arm is good. ***4) Smaller targets are captured with higher efficiency. ***5) Low GC content is better for both arms according to the Cosmic set. I still need to look at the CES22K set. ***6) Conclusions cannot really be drawn from the frequency data for the Cosmic set or the CES22K set, as the confidence interval is very very large. In general, the only thing I can see is that the ligation arm frequency should be higher. **'''Here is the finished PowerPoint:''' [[Media:Cosmic_CES22K_Presentation.ppt]] **Still need to add target GC content data and arm GC content from CES22K set. *'''Incorporating Effect Plots into Scoring''' **Effect plots have allowed each factor to have an equation fitting its value to output. **This allows these equations to be directly used in determining probe design. **Perhaps compare current scoring method (that uses match between oligos A and B in code) to output as well? **Then, would be able to determine how much to scale this factor as well as the other, already fit factors.
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