Table 1.
Nucleotide composition by structural context in the non-redundant bacterial and mmt SSU rRNA alignments
| Nucleotide composition in bacterial alignment (%) | |||||
|---|---|---|---|---|---|
| Structural Context | G | C | A | U | Total |
| Helix | 11.4 | 8.8 | 5.6 | 7.4 | 33.2 |
| Flanking | 11.0 | 8.6 | 3.3 | 4.7 | 27.6 |
| Loop | 9.4 | 5.1 | 16.2 | 8.5 | 39.2 |
| Total | 31.7 | 22.6 | 25.2 | 20.6 | 100.0 |
| Standard deviation of base composition across sequences in the alignment | 1.54 | 1.42 | 1.55 | 1.40 | |
| Nucleotide composition in mmt alignment (%) | |||||
| Structural Context | G | C | A | U | Total |
| Helix | 5.9 | 5.7 | 7.3 | 7.5 | 26.5 |
| Flanking | 8.2 | 8.3 | 6.7 | 6.1 | 29.3 |
| Loop | 4.3 | 8.7 | 21.5 | 9.6 | 44.2 |
| Total | 18.5 | 22.7 | 35.6 | 23.3 | 100.0 |
| Standard deviation of base composition across sequences in the alignment | 1.15 | 1.60 | 1.46 | 1.55 | |
The structural context is classified as Helix (for those nts within a helix), Flanking (for those nts at the ends of helices), and Loop (for internal or hairpin loops). The standard deviation is obtained, for example, by calculating the %G in each sequence of the alignment, and then calculating the standard deviation of those numbers.