Method for identifying nucleotide sequence, method for acquiring secondary structure of nucleic acid molecule, apparatus for identifying nucleotide sequence, apparatus for acquiring secondary structure of nucleic acid molecule, program for identifying nucleotide sequence, and program for acquiring secondary structure of nucleic acid molecule

An apparatus for preparing an optimized aptamer sequence, wherein said apparatus comprises a data processing device comprising a hardware processor and non-transitory computer-readable medium, said medium comprising one or more programs, executed by the hardware processor, which comprise commands for:

• (1) extracting data of a single-stranded region, by excluding bases capable of forming a stem structure from the sequence of the nucleic acid molecule;
• and
• (2) searching a motif sequence from the single-stranded region, by weighing the appearance frequency of a specific sequence in the extracted data with an evaluated value of the affinity of the nucleic acid molecule for the target substance,
• and wherein said apparatus is configured to prepare and output an aptamer sequence that contains the region binding to the target substance, but which lacks one or more corresponding nucleotides that are present in the nucleic acid molecule and which are unnecessary for binding to the target substance.

An apparatus for preparing an optimized aptamer sequence, wherein said apparatus comprises a data processing device comprising a hardware processor and non-transitory computer-readable medium, said medium comprising one or more programs, executed by the hardware processor, which comprise commands for:

• (1) extracting data of a single-stranded region, by excluding bases capable of forming a stem structure from the sequence of the nucleic acid molecule;
• (2) searching a motif sequence from the single-stranded region, by weighing the appearance frequency of a specific sequence in the extracted data with an evaluated value of the affinity of the nucleic acid molecule for the target substance;
• and
• (3) acquiring a general structure from a secondary structure of the nucleic acid molecule, based on the single-stranded region that accords with the motif sequence and based on bases forming the stem structure positioned at both ends of the single-stranded region,
• and wherein said apparatus is configured to prepare and output an aptamer sequence that contains the region binding to the target substance, but which lacks one or more corresponding nucleotides that are present in the nucleic acid molecule and which are unnecessary for binding to the target substance.

A non-transitory, computer-readable storage medium, storing a program for preparing an optimized aptamer sequence, wherein said program screens nucleic acid sequences by identifying a region within a nucleic acid molecule that binds to a target substance, and wherein said program executes the steps of:

• (1) extracting data of a single-stranded region, by excluding bases capable of forming a stem structure from the sequence of the nucleic acid molecule;
• (2) searching a motif sequence from the single-stranded region, by weighing the appearance frequency of a specific sequence in the extracted data with an evaluated value of the affinity of the nucleic acid molecule for the target substance;
• and
• (3) preparing and outputting an aptamer sequence that contains the region binding to the target substance, but which lacks one or more corresponding nucleotides that are present in the nucleic acid molecule and which are unnecessary for binding to the target substance.

A non-transitory, computer-readable storage medium, storing a program for preparing an optimized aptamer sequence, wherein said program screens nucleic acid sequences by acquiring a secondary structure of a nucleic acid molecule that contains a region that binds to a target substance, and wherein said program executes the steps of:

• (1) extracting data of a single-stranded region, by excluding bases capable of forming a stem structure from the sequence of the nucleic acid molecule;
• (2) searching a motif sequence from the single-stranded region, by weighing the appearance frequency of a specific sequence in the extracted data with an evaluated value of the affinity of the nucleic acid molecule for the target substance;
• (3) acquiring a general structure from a secondary structure of the nucleic acid molecule, based on the single-stranded region that accords with the motif sequence and based on bases forming the stem structure positioned at both ends of the single-stranded region;
• and
• (4) preparing and outputting an aptamer sequence that contains the region binding to the target substance, but which lacks one or more corresponding nucleotides that are present in the nucleic acid molecule and which are unnecessary for binding to the target substance.