| Â | C1 | C2 | C3 | C4 | C5 | C6 |
|---|
E. coli Sequence Data | Fulla | Fulla | Red.b | Red.b | Red. & Alignedc | Red. & Alignedc |
|---|
Indep. Species | No | Yes | No | Yes | No | Yes |
|---|
Crp Knownd | 1(2) | 7(10) | 1(2) | 8(12) | 4(6) | 11(16) |
Crp Noveld | 0(0) | 16(20) | 0(0) | 16(18) | 6(7) | 18(21) |
PurR Knownd | 1(1) | 9(9) | 1(1) | 11(11) | 9(9) | 12(12) |
PurR Noveld | 0(0) | 4(5) | 0(0) | 4(5) | 3(4) | 6(7) |
- This table shows the number of E. coli intergenic regions predicted by PhyloScan to contain Crp or PurR binding sites, with the total number of sites predicted within parentheses. Column C1 is for a scan of the full set of E. coli intergenic sequence data (excluding the S. typhi sequence data and the sequence data from the other, independent clades). Column C3 is for a scan of only that E. coli sequence that is alignable with S. typhi; the S. typhi sequence data continue to be excluded. Column C5 is for a scan of the aligned E. coli-S. typhi sequence data. Columns C2, C4, and C6, are like Columns C1, C3, and C5, respectively, but the sequence data from the independent clades are also incorporated. Observing the lack of improvement of Column C3 over Column C1 (or the meager improvement of C4 over C2), we conclude that there is minimal gain in sensitivity from considering only E. coli sequence that is alignable with S. typhi, when not actually using the aligned S. typhi sequence data. Observing the modest improvement of C5 over C3 (or C6 over C4), we conclude that incorporating the aligned S. typhi sequence gives a moderate gain in sensitivity. Observing the large improvement of C2 over C1 (or C4 over C3, or C6 over C5), we conclude that incorporating the data from species that are not alignable with E. coli gives a significant gain in sensitivity. Notes: aDatabase of 2379 intergenic sequences from E. coli [see Additional file 2]. bDatabase of E. coli sequences (reduced search space) extracted from the E. coli-S. typhi database (see Real Sequence Data in Results). cDatabase of E. coli-S. typhi aligned intergenic sequences (see Real Sequence Data in Results). dThe number of E. coli intergenic regions predicted by PhyloScan to contain Crp or PurR binding sites, where the total number of binding sites detected is in parentheses and those sites that correspond to known, experimentally verified transcription factor binding sites and those sites that are novel (not yet verified) are indicated.
