Additional file 1:

Test Datasets. A compressed archive (zip) containing: the rulesets used to generate the test-set datasets (ASCII/xml); the datasets in both Relos and fasta format (ASCII); and histograms of each test-set to provide an overview of the data (PNG).

Format: ZIP Size: 123KB Download file

Additional file 2:

Figure 2 Rule-sets. A compressed archive (zip) file containing the simulation files (ASCII/xml). used in the generation of figure 2.

Format: ZIP Size: 3KB Download file

Additional file 3:

Rule Specification and Promoter Analysis. Detailed information on how to specify rules and how promoters are analyzed.

Format: TXT Size: 24KB Download file

Additional file 4:

Supplementary Table 1: Relos Dependencies. A listing of modules needed for Relos to run and where they can be obtained.

Format: PDF Size: 48KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional file 5:

Relos Source Code. A compressed archive (zip) containing the perl source for running Relos, the xml document-type definitions (DTD) which define simulation files, example simulation files, the README, and the source license (GPL).

Format: ZIP Size: 100KB Download file

Additional file 6:

Image of modules from generated promoters. A "heat map" image showing the expression from the generated promoters. Promoters with only "Spacer" elements are not depicted.

Format: PNG Size: 24KB Download file

Additional file 7:

Sample Ruleset for Biological Comparison. Ruleset used in one of the 255 "microarray" simulations.

Format: XML Size: 4KB Download file

Additional file 8:

Ruleset Used for Promoter Generation. The ruleset used to generate the 1000 promoters used in testing the biological relevance of Relos-generated promoters.

Format: XML Size: 1KB Download file