Table 2.
Summary of sRNAPredict2 annotations for sRNA-encoding genes in 11 species of pathogens
| Speciesa | No. of BLAST partnersa | Total no. of sRNAs predictedb | No. of unique sRNAs predictedc | No. of novel sRNAs predictedd… | …conserved in >1 partner | …conserved in >2 partners | …encoding predicted conserved RNA structure | Total kb IGR conservatione | Proportion of previously annotated sRNAs predicted | No. of IG terminators | No. of unique sRNA/Mb genome | No. of unique sRNA/10 kb IGR | No. of unique sRNAs/IG terminator | No. of total sRNAs/100 kb IGR conservation |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| B.anthracis | 6 | 1828 | 947 | 889 | 688 | 23 | 858 | 1235.4 | 2/3 | 2895 | 181.1 | 12.73 | 0.327 | 14.80 |
| Y.pestis | 7 | 1478 | 772 | 755 | 443 | 221 | 550 | 1627.5 | 13/24 | 1201 | 167.8 | 9.45 | 0.643 | 10.62 |
| S.enterica | 7 | 1284 | 599 | 572 | 321 | 145 | 460 | 1486.3 | 22/39 | 1289 | 116.8 | 7.73 | 0.465 | 8.64 |
| Staphylococcus aureus | 3 | 344 | 168 | 144 | 84 | 48 | 106 | 366.2 | 3/4 | 819 | 59.8 | 3.36 | 0.205 | 9.39 |
| Clostridium tetani | 4 | 426 | 161 | 138 | 108 | 77 | 127 | 534.3 | 0/3 | 852 | 56.1 | 4.22 | 0.189 | 7.97 |
| Streptococcus pneumoniae | 5 | 111 | 63 | 62 | 29 | 13 | 48 | 78.8 | 0/3 | 675 | 29.2 | 2.52 | 0.093 | 14.08 |
| Streptococcus pyogenes | 5 | 126 | 62 | 56 | 26 | 19 | 49 | 247.1 | 2/3 | 613 | 33.5 | 2.28 | 0.101 | 5.10 |
| Mycobacterium tuberculosis | 4 | 78 | 56 | 56 | 13 | 6 | 47 | 199.6 | 0/3 | 114 | 12.7 | 1.75 | 0.491 | 3.91 |
| Helicobacter pylori | 6 | 130 | 50 | 50 | 42 | 29 | 8 | 114.6 | 0/3 | 126 | 29.9 | 3.60 | 0.397 | 11.35 |
| C.trachomatis | 5 | 51 | 43 | 43 | 4 | 3 | 30 | 81.2 | 0/3 | 167 | 41.3 | 4.58 | 0.257 | 6.28 |
| P.aeruginosa | 3 | 72 | 38 | 34 | 19 | 13 | 25 | 152.3 | 5/6 | 1018 | 6.1 | 0.59 | 0.037 | 4.73 |
| Total (10 genomesf) | 6073 | 2912 | 2759 | 1758 | 584 | 2308 | ||||||||
| Max. fold differenceg | 35.8 | 20.3 | 22.2 | 29.7 | 21.6 | 17.4 | 3.8 |
aStrain names of the species annotated and of their BLAST partners as well as the sources of their genomic sequence files are listed in Supplementary Table S2.
bThe total number of sRNA-encoding genes predicted in all searches between the species of interest and each of its BLAST partners.
cThe number of distinct sRNA-encoding genes predicted in the species of interest as determined by using the sRNAPredict2 Venn diagram function.
dThe number of predicted sRNAs that do not correspond to riboswitches or sRNAs annotated in the Rfam database.
eThe amount of genome sequence conserved between the species of interest and all partner species.
fNot including P.aeruginosa.
gThe fold difference between the largest and smallest values in each column.