PMC:1892782 / 19234-22929 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/1892782","sourcedb":"PMC","sourceid":"1892782","source_url":"https://www.ncbi.nlm.nih.gov/pmc/1892782","text":"Table 1 Evaluation of RNAstrand.\nc = 0 c = 0.5 c = 0.9\nncRNA type N a N c A A + A - A 1-A-u u A 1-A-u u A(RNAz)\nAlignments classified as structured RNA by RNAz\n5S rRNA 413 1 0.990 0.993 0.988 0.978 0.006 0.016 0.958 0.000 0.042 0.973\n5.8S rRNA 146 1 0.932 0.932 0.932 0.894 0.055 0.051 0.733 0.024 0.243 0.904\ntRNA 286 1 0.948 0.948 0.948 0.886 0.017 0.096 0.621 0.009 0.371 0.535\nmiRNA 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]\nsnoRNA (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]\nsnoRNA (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]\nspliceos. 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]\neuk. SRP RNA 891 1 0.997 0.998 0.996 0.992 0.001 0.007 0.972 0.000 0.028 0.841\nnucl. RNaseP 31 1 0.694 0.710 0.677 0.613 0.274 0.113 0.387 0.081 0.532 0.290\nRNase MRP 140 1 0.989 0.986 0.993 0.982 0.000 0.018 0.961 0.000 0.039 0.500\nIRES 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]\nSECIS 76 1 0.651 0.658 0.645 0.520 0.257 0.224 0.329 0.191 0.480 0.487\n7SK 184 1 0.041 0.043 0.038 0.024 0.916 0.060 0.011 0.802 0.188 0.038\nAlignments not classified as structured RNA by RNAz\n5S rRNA 525 1 0.793 0.821 0.766 0.717 0.130 0.153 0.552 0.057 0.390 -\n5.8S rRNA 1000 1 0.853 0.892 0.814 0.771 0.092 0.137 0.602 0.032 0.366 -\ntRNA 1 1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 -\nmiRNA 0 - - - - - - - - - - -\nsnoRNA (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] -\nsnoRNA (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] -\nspliceos. 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] -\neuk. SRP RNA 3 1 3/3 3/3 3/3 3/3 0/3 0/3 3/3 0/3 0/3 -\nnucl. RNaseP 2 1 2/2 2/2 2/2 2/2 0/2 0/2 1/2 0/2 1/2 -\nRNase MRP 0 - - - - - - - - - - -\nIRES 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] -\nSECIS 43 1 0.686 0.698 0.674 0.593 0.174 0.233 0.302 0.070 0.628 -\n7SK 630 1 0.127 0.152 0.102 0.063 0.798 0.139 0.018 0.640 0.342 -\nNa: number of alignments in test set, Nc: 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. 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