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Distributed representations for a pairwise alignment: a pair of one-hot codes of four nucleotides of RNA and the gap symbol and a three-dimensional vector for representing secondary-structure information specific to ncRNAs. The parentheses ‘(’ and ‘)’ represent the left side of a base pair and the right side of a base pair, respectively (This dot-bracket notation is a convenient way of representing secondary structure originally used in the Vienna RNA package (Hofacker, 2003).)
