Additional file 1:

Percentage of SD presence, preferred location for the SD motif, and 16S rRNA tail used of each prokaryote genome. Excel file showing the percentage of genes in each SD populations (see Materials and Methods), the optimal distance between the beginning of the SD motif and the first base of the start codon and the 16S rRNA tail used to calculate the binding between the 16S rRNA and the mRNA for each prokaryote chromosome. Taxonomical information for each prokaryote genome is also given. The 530 prokaryote chromosomes are sorted by the percentage of genes with a predicted SD sequence.

Format: XLS Size: 147KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 2:

Distribution of the spacing lengths by phylums. Excel file showing the distribution of the short spacing lengths up to 50 bps between the co-directional genes grouped by phylums.

Format: XLS Size: 88KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 3:

Statistical analysis of the SD presence. Word file showing the results of the ANOVA analysis to check whether the taxonomy and the distances between co-directional genes can affect the presence of the SD sequence. Post Hoc tests (Tukey test) were performed in both factors to determine which levels have differences. Significant differences have a P value < 0.05 and are denoted in bold.

Format: DOC Size: 144KB Download file

This file can be viewed with: Microsoft Word Viewer

Additional file 4:

Sequence logos for B. subtilis and T. kodakaraensis. Weblogos showing the SD pattern for B. subtilis when there is a distance between genes of 10 bps (9 genes considered) (A), and the SD pattern for T. kodakaraensis when there is a distance between genes of 6 bps (16 genes considered) (B). For each position (from -20 to 2 bps), the sequence logo shows the amount of information content and the frequency of nucleotides. The blank positions mean that there is no information content. Those with information content contain a stack of nucleotides. The size of the nucleotide character is proportional to its frequency at that position. Each sequence logo has the average of ΔG° values from -20 to 2 bps of the genes separated by each of the spacers analyzed. The higher the ΔG° value, the stronger the binding between the 16S rRNAs and the mRNAs. The drops in ΔG° values indicate where the 5'A of the 16S rRNA tail (3'-CCUCCA-5') can bind the SD sequence. These drops are before the SD patterns TAGGAGG in B. subtilis and on the T in the middle of the SD pattern GGTGA in T. kodakaraensis.

Format: TIFF Size: 293KB Download file

Additional file 5:

Comparison of the distances between co-directional genes calculated with NCBI annotations and with triTISA. Comparison of the distribution of the distances between co-directional genes calculated with the NCBI annotations and with the annotations refined with triTISA (A), and correlation between the intergenic distances calculated with the RefSeq annotations and with the annotations refined by the triTISA program (B). The figure shows the correlation coefficient and the linear equation.

Format: TIFF Size: 320KB Download file