"... In PAGE 12: ... The filled-in hxmatch prediction contains all helices for all six test cases. A comparison of hxmatch with RNAalifold and ilm is given in Table6 , and Figure 5 shows, as an example, the prediction results for RNase P RNA. These sequences are already too long to use pknots.... ..."

"... In PAGE 2: ... To reduce the likelihood that an amiRNA would actasprimerforRNA-dependent RNApolymerases, andthereby trigger secondary RNAi, between one and three mismatches to the target genes were introduced in the 39 part of the amiRNAs. See Table1 for a list of amiRNAs and intended targets, with alignments shown in Supplemental Figure 1 online. It was shown previously that both animal and plant miRNA precursors can be modified to express a small RNA with a sequence that is unrelated to the miRNA normally produced by the precursor (Zeng et al.... In PAGE 5: ..., 2004). amiR-mads-1 and amiR-mads-2 target 7 and 13 MADS box genes, respectively, that are mostly involved in the control of flowering time and floral patterning (Becker and Theissen, 2003), with a few additional non-MADS targets (see complete list in Supplemental Table1 online). amiR-yabby-1 and amiR-yabby-2 target different members of the YABBY gene family, with two predicted targets for amiR-yabby-1 and one for amiR-yabby-2.... In PAGE 6: ...iljegren et al., 2000). In the strongest lines, which also express more amiRNA than the weaker lines (see Supplemental Figure 4 online), carpels were replaced by a new inflorescence shoot. Expression analysis with Affymetrix microarrays showed that most predicted target genes were significantly downregulated in inflorescence tissue of both weak and strong overexpressers (Figure 4B; see Supplemental Table1 online). Plants overproducing amiR-yabby-1 and -2 had defects in leaf polarity, such as leaves with trichomes on both sides, indicating adaxialization (amiR-yabby-1; Figure 3G).... In PAGE 11: ... Supplemental Data The following materials are available in the online version of this article. Supplemental Table1 . Predicted Target Genes of Artificial Micro- RNAs and Expression Changes in amiRNA Overexpressers Com- pared with Wild-Type Controls by Microarray Analyses.... ..."

"... In PAGE 3: ... If only a few variables are relevant the LASSO has also the good property of shrinking the weights of irrelevant features to zero, therefore providing simpler interpretation of relevant features in the final model. Table1 shows the performance of the predictive linear models trained on the various sparse, spectral and composite representations. The performance is assessed in terms of Pearson correlation coefficient between the pre- dicted and the true efficacy for the 249 siRNAs in the test set, in order to provide a fair comparison with Huesken et al.... In PAGE 9: ...60 L1 norm of the LASSO weights Correlation Page 9 of 17 (page number not for citation purposes) energy profiles might be relevant features to help predict the efficacy of siRNA. Table1 shows the result of siRNA provide a useful benchmark to assess the validity of our... ..."

"... In PAGE 15: ... Since hxmatch is designed to have a high specifity, base pairs that are incompatible with more than half of the sequences of the dataset are not contained in the prediction. Table7 shows the quality of predictions for the same sequences that were used in Table 6, but this time using alignments generated by Clustalw. Pure sequence alignments with rather low similarity are only partially structurally correct.... ..."

"... In PAGE 7: ... Prediction accuracy using individual sequences The second set of experiments was carried out on a set of individual sequences to compare MWM, PKNOTS and ILM. The results are listed in Table3 . The score matrices used by ILM and MWM were calculated using the exten- ded helix plot with default parameters.... ..."