Table 1 The data sets used in this study. The first column contains a short name describing the data set, that is later used in text and figures. The RNA families/data sets can contain several types of sequences, such as the RNase family that contains both RNase P and RNase MRP. The different sequence types, or family members, are given in column two. In column three and four the number of family members (N FM ) and the total number of sequences (N S ) are given, respectively. The last two columns in the table give the mean and standard deviation of the sequence length and %GC-content.
short name (full name) | family members | N S | length | % GC |
|---|---|---|---|---|
miRNA (microRNA) | all 38 miRNAs in Rfam | 135 | 82.82 ± 16.01 | 46.01 ± 7.44 |
intron | group I and II | 107 | 148.03 ± 113.72 | 43.24 ± 10.33 |
RNase | RNase P and MRP | 147 | 320.89 ± 37.80 | 56.70 ± 9.88 |
SRP (signal recognition particle) | bacterial and eukaryotic/archae SRP | 77 | 187.14 ± 100.47 | 58.27 ± 10.44 |
rRNA (ribosomal RNA) | small subunit and 5S rRNA | 578 | 380.06 ± 196.50 | 50.93 ± 8.37 |
snRNA (small nuclear spliceosomal RNA) | all 8 spliceosomal snRNAs in Rfam | 82 | 135.22 ± 39.40 | 47.19 ± 6.69 |
riboswitch | lysine, s-box (SAM riboswitch), cobalamin | 154 | 175.87 ± 49.59 | 51.38 ± 10.33 |
tmRNA | 59 | 345.03 ± 32.18 | 45.48 ± 10.07 | |
regulatory | IRE, IRES, SECIS, HIV primer binding site, VARNA | 17 | 80.62 ± 56.24 | 49.78 ± 10.21 |
tRNA (transfer RNA) | 565 | 73.16 ± 5.41 | 46.94 ± 12.02 | |
telomerase | 17 | 442.53 ± 41.23 | 64.49 ± 6.98 | |
snoRNA (small nucleolar RNA) | all 177 guide snoRNAs in Rfam | 412 | 97.60 ± 39.64 | 43.38 ± 7.43 |
Hh1 (Hammerhead ribozyme (type I)) | 16 | 54.44 ± 24.08 | 49.49 ± 8.03 | |
mRNA (messenger RNA) | 32 | 329.94 ± 90.33 | 49.98 ± 8.47 | |
shuffled (control data set) | 130 | 199.86 ± 154.01 | 50.33 ± 10.61 |