Sequence matching algorithms and pairing of noncoding RNAs
S. K. Nechaev,
M. V. Tamm,
O. V. Valba
Abstract:A new statistical method of alignment of two heteropolymers which can form hierarchical cloverleaf-like secondary structures is proposed. This offers a new constructive algorithm for quantitative determination of binding free energy of two noncoding RNAs with arbitrary primary sequences. The alignment of ncRNAs differs from the complete alignment of two RNA sequences: in ncRNA case we align only the sequences of nucleotides which constitute pairs between two different RNAs, while the secondary structure of eac… Show more
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