Probe designing method and information processing apparatus

• US 7,254,488 B2
• Filed: 02/22/2002
• Issued: 08/07/2007
• Est. Priority Date: 02/28/2001
• Status: Expired due to Fees

• Current Assignee: Canon Kabushiki Kaisha (Canon Inc.)
• Original Assignee: Canon Kabushiki Kaisha (Canon Inc.)
• Inventors: Yoshii, Hiroto
• Primary Examiner(s): Brusca; John S.
• Assistant Examiner(s): Lin; Jerry
• Application Number:
  US10/081,554
• Publication Number:
  US 20030008303A1
• Time in Patent Office: 1,992 Days
• Field of Search: 702/19, 702/20
• US Class Current: 702/19
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 25/20 Polymerase chain reaction [PCR]; Primer or probe design; Probe optimisation

Abstract

In automatically designing a base sequence to be used as a probe which is hybridized with an unknown nucleic acid fragment to perform gene analysis, a discrimination tree in which a plurality of partial base sequences obtained from target base sequence data are arranged on nodes is generated. The suitability as a probe of a partial base sequence represented by a desired node is evaluated. A plurality of partial base sequences are grouped on the basis of specificity, and an appropriate group combination is selected. A partial base sequence to be used as a probe is determined, from partial base sequences belonging to the selected groups, on the basis of the evaluation result. In this manner, a probe appropriate for analysis can be automatically selected in accordance with a target base sequence to be analyzed. This effectively supports probe designing.

Claims

1. 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.

2. The method according to claim 1, wherein the plurality of partial base sequences in the generation step are partial base sequences obtained from a complementary base sequence of the target base sequence.

3. The method according to claim 1, wherein

the plurality of partial base sequences in the generation step are partial base sequences obtained from the target base sequence, and

the determination step comprises selecting a partial base sequence on the basis of the evaluation result in the evaluation step, and determining a complementary base sequence of the selected partial base sequence as a partial base sequence to be used as a probe.

4. The method according to claim 1, wherein the generation step comprises generating a tree for typing all partial base sequences obtained on the basis of the target base sequence.

5. The method according to claim 1, wherein the evaluation step comprises introducing an evaluation function which, when a base sequence whose specificity with respect to the target changes over a predetermined amount exists at the center of a partial base sequence, gives the partial base sequence an evaluation result to be determined to be used as a probe in the determination step.

6. The method according to claim 5, wherein the determination step comprises determining, as a probe, a partial base sequence corresponding to a node whose value calculated by the evaluation function in the evaluation step exceeds a predetermined value.

7. The method according to claim 1, wherein the determination step comprises determining, as a probe, a partial base sequence corresponding to a node whose change in the entropy exceeds a predetermined value.

8. The method according to claim 1, further comprising the grouping step of grouping the plurality of partial base sequences in accordance with specificity with respect to the target base sequence,

wherein the determination step comprises determining a partial base sequence to be used as a probe from each group on the basis of the evaluation result in the evaluation step.

9. The method according to claim 1, further comprising:

the grouping step of grouping the plurality of partial base sequences in accordance with specificity with respect to the target base sequence; and

the selecting step of selecting a group having specificity appropriate as a probe from groups obtained in the grouping step,

wherein the determination step comprises determining a partial base sequence to be used as a probe, from each group selected in the selecting step, on the basis of the evaluation result in the evaluation step.

10. The method according to claim 9, wherein the selecting step comprises eliminating at least a group having no specificity with respect to all targets to be analyzed.

11. The method according to claim 9, wherein the evaluation step comprises evaluating partial base sequences in a group selected in the selecting step.

12. The method according to claim 8, wherein the target contains a plurality of base sequence patterns, and

the grouping step comprises assigning, to the same group, partial base sequences which react to the same base sequence patterns.

13. The method according to claim 1, wherein in the tree, the base sequence order of partial base sequences represented by node connections is identified with the base sequence order in the target.

14. The method according to claim 1, wherein in the tree, the base sequence order of partial base sequences represented by node connections is changed such that the central one of corresponding partial base sequences in the target is the first one.

15. The method according to claim 1, wherein the evaluation step comprises evaluating only a partial base sequence having a length within a previously designated range.

16. The method according to claim 1, wherein the evaluation step comprises evaluating only a partial base sequence meeting a melting temperature condition within a previously designated range.

17. The method according to claim 1, wherein the determination step comprises determining a partial base sequence as a probe, from partial base sequences having lengths within a previously designated range, on the basis of the evaluation result in the evaluation step.

18. The method according to claim 1, wherein the determination step comprises determining a partial base sequence as a probe, from partial base sequences meeting a melting temperature condition within a previously designated range, on the basis of the evaluation result in the evaluation step.

20. A storage medium storing a program adapted to control a computer to perform the method of determining a probe candidate according to claim 1.

21. A method of designing a probe including the steps of determining and outputting a probe candidate in accordance with claim 1, and using the probe candidate to design a probe.

19. An information processing apparatus for performing the method of determining 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, said apparatus comprising:

generation means for 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;

extraction means for 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;

evaluation means for 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;

determination means for 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 said evaluation means; and

wherein said evaluation means calculates 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, introduces 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 obtains an evaluation result based on a calculation result of the evaluation function.