AlexLabNotebook/ChrIIIRebuild

No longer working on this.

= Chromosome rebuild = Assertion: Will rebuild chromosome III, because that's the one that's best-studied

Proposed schedule:
 * Complete chr III independent functional element list by 10/7
 * Put together ~20K long sequence for pilot project by 10/14
 * Figure out actual recombination & selection steps, send sequence out for synthesis by 10/30

Currently working on: Making list of independent functional elements.

Calendar

 * 09/05
 * 9/19/05-9/23/05: Made list of all features on chromosome III, started to gather data about how to define 5' and 3' ends of genes.
 * 9/24/05-9/30/05: Generated initial list of overlapping regions, figured out flanking sequences needed for Ty elements [none], sent gene sequences off to Joel Graber for 3' end prediction, started to look into ways to define 5' gene ends.
 * 10/05
 * 10/1/05-10/7/05: Downloaded conservation scores for [almost] all positions on chr III, generated conservation "profile" for all intergenic regions, used Pychart to generate plots of these profiles.
 * 10/8/05-10/14/05