miRNA display CGI


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ID Location Perfect MFE.* RefSeq Acc. strand Start Position R_P_ratio# P value
Predicted miRNA align pattern
9564 5' -49.3 NC_002554.1 + 6495 0.66 0.417217
Target:  5'- cGUUGGCacucacucugCUGGaGGCAAUGGAGUUgGGu -3'
miRNA:   3'- uUAGCCG----------GAUC-CUGUUAUCUCAAgUC- -5'
9564 5' -49.3 NC_002554.1 + 5739 0.69 0.293725
Target:  5'- cAGUCGGCU--GGGCGGgcucAGAGUUCAc -3'
miRNA:   3'- -UUAGCCGGauCCUGUUa---UCUCAAGUc -5'
9564 5' -49.3 NC_002554.1 + 3773 1.06 0.00038
Target:  5'- gAAUCGGCCUAGGACAAUAGAGUUCAGc -3'
miRNA:   3'- -UUAGCCGGAUCCUGUUAUCUCAAGUC- -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.