Additional supplementary data for paper "A Three-Dimensional Model of the Yeast Genome"

• HindIII interactions at FDR 1%      [ intra >=20kb | inter ]
• HindIII interactions at FDR 0.1%   [ intra >=20kb | inter ]
• HindIII interactions at FDR 0.01% [ intra >=20kb | inter ]
• HindIII interactions overlapped with EcoRI interactions at FDR 0.01% [ intra >=20kb | inter ]
  
  
• HindIII + MspI interactions before FDR   [ intra >=20kb | intra all | inter ]  (this corresponds to column 4 of Sup. Table 4)
• HindIII + MseI interactions before FDR   [ intra >=20kb | intra all | inter ]  (this corresponds to column 4 of Sup. Table 4)
  
• EcoRI + MspI interactions before FDR   [ intra >=20kb | intra all | inter ]
• EcoRI + MseI interactions before FDR   [ intra >=20kb | intra all | inter ]
  
  
• HindIII + MseI un-cross-linked interactions (no FDR)   [ intra >=20kb | intra all | inter ]  

• PDB file (can be visualized with Rasmol)
• Rasmol script to obtain Figure 5a (at the rasmol prompt, run "script rasmol_color_rotation1.script")
• Rasmol script to obtain Figure 5b (at the rasmol prompt, run "script rasmol_color_rotation2.script")
• Text file with genomic positions and 3D coordinates. To obtain the 3D coordinate of a particular locus, look for the closest locus that appears in this file. This file can be used to obtain the physical distance (in nm), according to our model, between specific genomic loci. Note that the ribosomal DNA repeats in chromosome XII appear only twice in the reference genome, but in vivo this region is repeated 100-200 times. So we added this region 148 times to obtain 150 repeats. The length of the region is 9100 bases, and the position is 451000. In other words, our chromosome XII is 148*9100 bases longer than the reference genome. All the genes that have locations greater than 451000 in the reference genome should have 148*9100 bases added to their coordinates to obtain the correspondence to our genes.
• Code for generating the 3D model

• Text file with the tRNA ID's, positions and clusters

• The clusters we obtained for early origins
• Coordinates of early origins nonCDR (chromosome, start, end)
• Coordinates of late origins CDR (chromosome, start, end)
• Coordinates of early origins unchecked (chromosome, start, end)
• Coordinates of late origins checked (chromosome, start, end)

• HindIII
• EcoRI
• Columns are: (1) chromosome; (2) Position of the RE site; (3) whether it is mappable (0=no, 1=yes); (4) the mid-fragment to the left; (5) the mid-fragment to the right

• Scripts and configuration files for generating the Circos diagrams

Note that the version of the yeast genome used for our analyses was gi|144228165|ref|NC_001133.7.