miRNA display CGI


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Acc. No. Name Perfect MFE.* RefSeq Acc. strand Start Position R_P_ratio# P value
Predicted miRNA align pattern
MIMAT0002193 kshv-miR-K12-3 -48.9 NC_003409.1 + 102147 0.66 0.98615
Target:  5'- aGCUGCgGUCuCUCGGcuuccgcGUGUGAu -3'
miRNA:   3'- gCGACGgCAG-GAGUCu------UACACU- -5'
MIMAT0002193 kshv-miR-K12-3 -48.9 NC_003409.1 + 34186 0.7 0.926585
Target:  5'- gGC-GaCCGUCgUCAGggUGUGAg -3'
miRNA:   3'- gCGaC-GGCAGgAGUCuuACACU- -5'
MIMAT0002193 kshv-miR-K12-3 -48.9 NC_003409.1 + 121465 1.01 0.022956
Target:  5'- uCGCUGCCGUCCUCAGAAUGUGAu -3'
miRNA:   3'- -GCGACGGCAGGAGUCUUACACU- -5'
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Note:
      When operating RNAhybrid, the pipeline first calculates the perfect minimum free energy (Perfect mfe *) of a putative miRNA when the entire putative miRNA binds to a perfectly complementary target site, then it calculates the minimum free energy of RNA duplex (mfe of the miRNA/mRNA duplex), abbreviated as Rd_mfe. An alignment for which the Rd_mfe to its correspondent Perfect mfe ratio (R_P_ratio #) is more than 66% is regarded as a positive alignment as described by Krek et al. (21). The P_value is calculated by RNAhybrid.

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TDL, Institute of Biomedical Science, Academia Sinica, Taipei, Taiwan.
Copyright © 2007 TDL. All rights reserved.