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
2341 3' -51.2 NC_001416.1 + 10546 0.66 0.882328
Target:  5'- ---aGGCgAUCUGgUCGUUgauuuGAGUCUGg -3'
miRNA:   3'- gagaCCGgUAGACgAGCAG-----UUUAGAC- -5'
2341 3' -51.2 NC_001416.1 + 45947 0.71 0.611823
Target:  5'- gCUCUGGUUAUCUGCaucaUCGUCugccuGUCa- -3'
miRNA:   3'- -GAGACCGGUAGACG----AGCAGuu---UAGac -5'
2341 3' -51.2 NC_001416.1 + 10655 1.1 0.001568
Target:  5'- aCUCUGGCCAUCUGCUCGUCAAAUCUGg -3'
miRNA:   3'- -GAGACCGGUAGACGAGCAGUUUAGAC- -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.