METHOD OF PREDICTING NUCLEIC ACID HIGHER-ORDER STRUCTURE, APPARATUS FOR PREDICTING NUCLEIC ACID HIGHER-ORDER STRUCTURE, AND PROGRAM FOR PREDICTING NUCLEIC ACID HIGHER-ORDER STRUCTURE
The object of the present invention is to provide a method of predicting a higher-order structure of a nucleic acid sequence typified by a G quartet structure, and an apparatus and a program that execute the method. The method according to the present invention relates to a method of predicting a nucleic acid higher-order structure that predicts a higher-order structure of a nucleic acid sequence, the method, including the steps of: extracting bases capable of forming a higher-order structure as a higher-order structure candidate from said nucleic acid sequence; extracting bases capable of forming a stem structure as a stem structure candidate from said nucleic acid sequence; and searching an optimal combinatorial structure based on the higher-order structure candidate and the stem structure candidate.
1 . A method of predicting a nucleic acid higher-order structure that predicts a higher-order structure of a nucleic acid sequence, the method, comprising the steps of:
extracting bases capable of forming a higher-order structure as a higher-order structure candidate from said nucleic acid sequence;
extracting bases capable of forming a stem structure as a stem structure candidate from said nucleic acid sequence; and
searching an optimal combinatorial structure based on the higher-order structure candidate and the stem structure candidate.
2 . The method of predicting a nucleic acid higher-order structure according to claim 1 , wherein the step of searching the optimal combinatorial structure is a step in which, among combinatorial structures obtained by singularly or randomly combining the higher-order structure candidate and/or the stem structure candidate, a combinatorial structure giving a minimum free energy is assigned as said optimal combinatorial structure where no contradiction is present among bases of the higher-order structure candidate and the stem structure candidate.
3 . The method of predicting a nucleic acid higher-order structure according to claim 1 or 2 , further comprising the step of quantifying a relationship between a plurality of nucleic acid sequences, wherein the plurality of nucleic acid sequences is said nucleic acid sequence
4 . The method of predicting a nucleic acid higher-order structure according to claim 3 , wherein the step of quantifying the relationship between the plurality of nucleic acid sequences is a step in which a degree of conservation between the plurality of nucleic acid sequences is calculated.
5 . The method of predicting a nucleic acid higher-order structure according to claim 3 or 4 , wherein the plurality of nucleic acid sequences is evolutionarily conserved.
6 . The method of predicting a nucleic acid higher-order structure according to any one of claims 1 to 5 , wherein the higher-order structure is a G quartet.
7 . An apparatus for predicting a nucleic acid higher-order structure that predicts a higher-order structure of a nucleic acid sequence, the apparatus, comprising:
a higher-order structure candidate-extracting unit that extracts, from said nucleic acid sequence, bases capable of forming a higher-order structure as a higher-order structure candidate;
a stem structure candidate-extracting unit that extracts, from said nucleic acid sequence, bases capable of forming a stem structure as a stem structure candidate; and
an optimal structure-searching unit that searches an optimal combinatorial structure, based on the higher-order structure candidate and the stem structure candidate.
8 . The apparatus for predicting a nucleic acid higher-order structure according to claim 7 , wherein, among combinatorial structures obtained by singularly or randomly combining the higher-order structure candidate and/or the stem structure candidate, the optimal structure-searching unit assigns a combinatorial structure giving the lowest free energy as said optimal structure where no contradiction is present among bases of the higher-order structure candidate and the stem structure candidate
9 . The apparatus for predicting a nucleic acid higher-order structure according to claim 7 or 8 , further comprising an input sequence comparison unit that quantifies a relationship between a plurality of nucleic acid sequences, wherein the plurality of nucleic acid sequences is said nucleic acid sequence.
10 . The apparatus for predicting a nucleic acid higher-order structure according to claim 9 , wherein the input sequence comparison unit calculates a degree of conservation between the plurality of nucleic acid sequences.
11 . The apparatus for predicting a nucleic acid higher-order structure according to claim 9 or 10 , wherein the plurality of nucleic acid sequences is evolutionarily conserved.
12 . The apparatus for predicting a nucleic acid higher-order structure according to any one of claims 7 to 11 , wherein the higher-order structure is a G quartet.
13 . A program for predicting a nucleic acid higher-order structure that predicts a higher-order structure of a nucleic acid sequence, the program, executing the steps of:
extracting bases capable of forming a higher-order structure as a higher-order structure candidate from said nucleic acid sequence;
extracting bases capable of forming a stem structure as a stem structure candidate from said nucleic acid sequence; and
searching an optimal combinatorial structure based on the higher-order structure candidate and the stem structure candidate.
14 . The program for predicting a nucleic acid higher-order structure according to claim 13 , wherein the step of searching the optimal combinatorial structure is a step in which, among combinatorial structures obtained by singularly or randomly combining the higher-order structure candidate and/or the stem structure candidate, a combinatorial structure giving a minimum free energy is assigned as said optimal combinatorial structure where no contradiction is present among bases of the higher-order structure candidate and the stem structure candidate.
15 . The program for predicting a nucleic acid higher-order structure according to claim 13 or 14 , further executing the step of quantifying a relationship between a plurality of nucleic acid sequences, wherein the plurality of nucleic acid sequences is said nucleic acid sequence.
16 . The program for predicting a nucleic acid higher-order structure according to claim 15 , wherein the step of quantifying the relationship between the plurality of nucleic acid sequences is a step in which a degree of conservation between the plurality of nucleic acid sequences is calculated.
17 . The program for predicting a nucleic acid higher-order structure according to claim 15 or 16 , wherein the plurality of nucleic acid sequences is evolutionarily conserved.
18 . The program for predicting a nucleic acid higher-order structure according to any one of claims 13 to 17 , wherein the higher-order structure is a G quartet.