AlexLabNotebook/ChrIIIRebuild/10/1/05-10/7/05

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10/1/05 - 10/7/05

Last week: 9/24/05-9/30/05

Next week: 10/8/05-10/14/05

Goals this week:

  • Figure out flanking sequences necessary for ncRNA function -- still not done
  • Make initial attempt at using conservation to figure out 5' flanking sequence for genes -- Have conservation data and intergenic regions, need to write code to calculate high-scoring islands
  • Think some more about canonical promoters + using Eran Segal's method -- didn't happen

Canonical promoters

  • Take 5' conserved sequence + specific Pol II promoter with well-identified TATA box etc and use that as promoter in front of all the genes ?
  • Conservation data from Adam Siepel in David Haussler's group. Downloaded conservation scores, will use these to plot score profiles for all the intergenic regions to help figure out which bits of intergenic sequence to include in defining each gene

Visualization

Intergenic sections of chrIII

Generated by interfeatureregions.py

List of all sections of the chromosome that are in between genes [but may overlap with other elements, like ARS etc], plus 100 bases on either end to show flanking genes:

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