PMC:1892782 / 18271-19233 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 lists the classification rates for different threshold values c, i.e., classifying the RNA as \"plus strand\" for D \u003e c and as \"minus strand\" for D \u003c -c, while -c ≤ D ≤ c is interpreted as \"undecided\". We observe only a negligible loss of accuracy when c is increased from 0 to 0.9. The distribution of D (see Additional file 1) demonstrates that the majority of alignments are classified correctly with high probability. However, RNAstrand fails to predict the correct reading direction of 53 families (e.g. 7SK). The predicted secondary structure of the reverse complementary alignment is much more stable for these examples than the ncRNA itself (see Additional file 1). On the other hand, RNAstrand is able to reliably capture the reading direction of most ncRNAs for which no representative was given in the training set, including RNase MRP, IRES, SECIS and 5.8S rRNA, which makes it suitable to predict the reading direction of novel ncRNA families.","tracks":[]}