Exact(3)
The miRNA duplex consists of the mature miRNA and its near complementary miRNA* strand.
Each novel miRNA had a corresponding near complementary sequence, referred as miRNA star (miRNA*).
Only a single strand (mature miRNA) is loaded into RNA-induced silencing complex (RISC) while a near complementary strand, miRNA star (miRNA*), is degraded [ 54, 55].
Similar(57)
Consequently, our goal here is to search for near-complementary regions.
However, when searching for near-complementary regions, the energy model of RNAplex can be simplified further.
miRNA can bind to the 3' UTR of a near-complementary sequence of mRNA and lead to reduced translation.
RIsearch is a fast method to search for near-complementary base pairing in genomic sequence by using a simplified energy model.
We show in benchmarks that we achieve a speed improvement of at least 2.4× compared with RNAplex, the currently fastest method for searching near-complementary regions.
We show that this energy model is an accurate approximation of the full energy model for near-complementary RNA RNA duplexes.
When the N-strand successfully rebinds to the T-strand, mispairing between complementary or near-complementary sequences would occur easily due to possible single strand folding.
These RNAs are processed from complementary or near-complementary double-stranded RNAs (dsRNAs) precursors into 21- to 26-nt RNAs by Dicer or Drosha RNase III family endonucleases in the cytoplasm (Bernstein et al. 2001; Lee et al. 2003).
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