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Results: 5

1.
Figure 5

Figure 5. From: Target prediction for small, noncoding RNAs in bacteria.

Northern analysis of predicted OxyS targets. MG1655 ΔoxyS::cm cells carrying pKK177-3 or poxyS were grown to late exponential phase (A600 ∼ 0.7). Total RNA isolated from these samples was probed with oligonucleotides complementary to the indicated genes.

Brian Tjaden, et al. Nucleic Acids Res. 2006;34(9):2791-2802.
2.
Figure 4

Figure 4. From: Target prediction for small, noncoding RNAs in bacteria.

Northern analysis of the predicted OmrB target gntP. MG1132 (carrying the ΔuxuR::cm allele) cells carrying pBR-plac, pBR-plac-OmrA or pBR-plac-OmrB were grown to midexponential phase (A600 ∼0.4) and half of the sample was treated with IPTG for 7 min. Total RNA isolated from these samples was probed with oligonucleotides complementary to the indicated genes.

Brian Tjaden, et al. Nucleic Acids Res. 2006;34(9):2791-2802.
3.
Figure 1

Figure 1. From: Target prediction for small, noncoding RNAs in bacteria.

The figure depicts the secondary structure for the sRNA RyhB. The Sm-like protein Hfq binds to the AU-rich unstructured region of RyhB as indicated. Below the secondary structure, the primary sequence of RyhB is shown along with its putative binding interaction to the target mRNA sodB (42). The start codon for sodB is underlined. RyhB nucleotides that participate in the interaction are in bold.

Brian Tjaden, et al. Nucleic Acids Res. 2006;34(9):2791-2802.
4.
Figure 2

Figure 2. From: Target prediction for small, noncoding RNAs in bacteria.

The graph shows the cumulative distribution function of hybridization scores for the sRNA RyhB. The curve on the right represents the hybridization scores calculated for RyhB against a message search space consisting of messages 50 nt in length (corresponding to a neighborhood around the ribosome-binding site). The curve on the left represents the hybridization scores calculated for RyhB against a message search space consisting of entire messages. Consequently, a hybridization score of −60 when searching messages 50 nt in length would lead to a significant P-value (<0.01), whereas a hybridization score of −60 when searching entire messages would not be significant.

Brian Tjaden, et al. Nucleic Acids Res. 2006;34(9):2791-2802.
5.
Figure 3

Figure 3. From: Target prediction for small, noncoding RNAs in bacteria.

ROC curves depict the trade-offs in sensitivity (ordinate) and false positive rate (abscissa) on the training dataset. Each ROC curve is generated from 21 data points, as the initial seed of interaction is set to a value ranging from 0 to 20 nt. The four ROC curves correspond to different combinations of parameters, including allowing G:U wobble pairs in the hybridization seed, disallowing G:U pairs in the seed, removing the terminator loop from the hybridization score calculation and retaining the terminator loop. Default parameter settings correspond to the top left point among the ROC curves.

Brian Tjaden, et al. Nucleic Acids Res. 2006;34(9):2791-2802.

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