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Table 1 Evaluation of RNAstrand.

From: RNAstrand: reading direction of structured RNAs in multiple sequence alignments

     c = 0    c = 0.5    c = 0.9   
ncRNA type N a N c A A + A - A 1-A-u u A 1-A-u u A(RNAz)
Alignments classified as structured RNA by RNAz
5S rRNA 413 1 0.990 0.993 0.988 0.978 0.006 0.016 0.958 0.000 0.042 0.973
5.8S rRNA 146 1 0.932 0.932 0.932 0.894 0.055 0.051 0.733 0.024 0.243 0.904
tRNA 286 1 0.948 0.948 0.948 0.886 0.017 0.096 0.621 0.009 0.371 0.535
miRNA 1875 43 0.981 [0.241] 0.979 [0.246] 0.982 [0.238] 0.965 [0.261] 0.009 [0.171] 0.026 [0.147] 0.906 [0.373] 0.001 [0.003] 0.094 [0.372] 0.187 [0.376]
snoRNA (C/D) 946 71 0.780 [0.376] 0.785 [0.374] 0.775 [0.389] 0.732 [0.411] 0.190 [0.363] 0.078 [0.256] 0.618 [0.431] 0.147 [0.286] 0.235 [0.416] 0.654 [0.446]
snoRNA (H/ACA) 3066 53 0.909 [0.198] 0.908 [0.198] 0.909 [0.199] 0.882 [0.255] 0.062 [0.160] 0.056 [0.184] 0.823 [0.352] 0.021 [0.039] 0.156 [0.339] 0.899 [0.283]
spliceos. RNA 896 6 0.877 [0.252] 0.885 [0.251] 0.868 [0.254] 0.831 [0.327] 0.086 [0.212] 0.083 [0.118] 0.735 [0.322] 0.042 [0.125] 0.222 [0.202] 0.835 [0.257]
euk. SRP RNA 891 1 0.997 0.998 0.996 0.992 0.001 0.007 0.972 0.000 0.028 0.841
nucl. RNaseP 31 1 0.694 0.710 0.677 0.613 0.274 0.113 0.387 0.081 0.532 0.290
RNase MRP 140 1 0.989 0.986 0.993 0.982 0.000 0.018 0.961 0.000 0.039 0.500
IRES 170 8 0.715 [0.453] 0.718 [0.455] 0.712 [0.452] 0.647 [0.469] 0.200 [0.424] 0.153 [0.339] 0.597 [0.448] 0.106 [0.433] 0.297 [0.402] 0.318 [0.424]
SECIS 76 1 0.651 0.658 0.645 0.520 0.257 0.224 0.329 0.191 0.480 0.487
7SK 184 1 0.041 0.043 0.038 0.024 0.916 0.060 0.011 0.802 0.188 0.038
Alignments not classified as structured RNA by RNAz
5S rRNA 525 1 0.793 0.821 0.766 0.717 0.130 0.153 0.552 0.057 0.390 -
5.8S rRNA 1000 1 0.853 0.892 0.814 0.771 0.092 0.137 0.602 0.032 0.366 -
tRNA 1 1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 -
miRNA 0 - - - - - - - - - - -
snoRNA (C/D) 4228 105 0.563 [0.397] 0.595 [0.399] 0.532 [0.414] 0.480 [0.420] 0.353 [0.363] 0.167 [0.236] 0.340 [0.394] 0.245 [0.316] 0.415 [0.364] -
snoRNA (H/ACA) 1993 36 0.788 [0.251] 0.812 [0.244] 0.763 [0.291] 0.735 [0.314] 0.157 [0.203] 0.108 [0.233] 0.644 [0.370] 0.081 [0.169] 0.274 [0.339] -
spliceos. RNA 2944 4 0.632 [0.287] 0.669 [0.287] 0.595 [0.289] 0.560 [0.314] 0.301 [0.261] 0.139 [0.071] 0.422 [0.338] 0.203 [0.200] 0.375 [0.180] -
euk. SRP RNA 3 1 3/3 3/3 3/3 3/3 0/3 0/3 3/3 0/3 0/3 -
nucl. RNaseP 2 1 2/2 2/2 2/2 2/2 0/2 0/2 1/2 0/2 1/2 -
RNase MRP 0 - - - - - - - - - - -
IRES 265 13 0.506 [0.454] 0.521 [0.454] 0.491 [0.454] 0.468 [0.411] 0.457 [0.450] 0.075 [0.276] 0.436 [0.401] 0.353 [0.411] 0.211 [0.418] -
SECIS 43 1 0.686 0.698 0.674 0.593 0.174 0.233 0.302 0.070 0.628 -
7SK 630 1 0.127 0.152 0.102 0.063 0.798 0.139 0.018 0.640 0.342 -
  1. N a : number of alignments in test set, N c : number of different RNA classes, A: accuracy, which is defined as the fraction of correctly classified input alignments, A+: accuracy of alignments in reading direction of ncRNA, A-: accuracy of reverse complementary alignments, u: fraction of undecided alignments, 1 - A - u: fraction of misclassified alignments, A(RNAz): fraction of alignments correctly classified by taking the strand with the largest RNAz probability as the strand of the ncRNA. Standard deviations for RNA families with alignments from different classes are given in brackets. Note, that in case c = 0 no undecided alignments are observed.