Patent ID: 7254488

Claim:
A method of determining and outputting a probe candidate that is utilized for designing a base sequence to be used as a probe which is hybridized with a nucleic acid fragment to perform analysis, comprising: a generation step of generating a tree in which a plurality of partial base sequences obtained on the basis of a plurality of target base sequences are arranged on nodes, said target base sequences including a base sequence to be examined; an extraction step of extracting a partial base sequence indicated by nodes present on a path from one of the nodes to a root node on the tree, the partial base sequence being a portion of the base sequence to be examined; an evaluation step of calculating specificity of the extracted partial base sequence among the plurality of target sequences, evaluating suitability as a probe of the extracted base sequence based on the calculated specificity and obtaining an evaluation result thereof; a determination step of determining a partial base sequence as a probe candidate that is utilized for designing a base sequence to be used as a probe which is hybridized with a nucleic acid fragment to perform analysis on the basis of the evaluation result in the evaluation step; and wherein the evaluation step comprises: calculating the entropy of each node present on the path as the specificity on the basis of the number of times of appearance of a partial base sequence corresponding to the node in the target base sequences; introducing an evaluation function which multiplies a change in the entropy between nodes by a weight which reduces in response to the increase of distance between the center of a partial base sequence and a node; and obtaining an evaluation result based on a calculation result of the evaluation function.