Probe designing apparatus and probe designing method

• US 7,035,738 B2
• Filed: 05/07/2002
• Issued: 04/25/2006
• Est. Priority Date: 05/29/2001
• Status: Expired due to Fees

• Current Assignee: Hitachi Software Engineering Co., Ltd. (Hitachi, Ltd.)
• Original Assignee: Hitachi Software Engineering Co., Ltd. (Hitachi, Ltd.)
• Inventors: Tamura, Takuro, Nozaki, Yasuyuki, Nakashige, Ryo, Ueno, Shingo, Matsumoto, Toshiko
• Primary Examiner(s): Zeman, Mary K.
• Application Number:
  US10/141,099
• Publication Number:
  US 20030069701A1
• Time in Patent Office: 1,449 Days
• Field of Search: 702/19, 702/20, 435/6, 536/23.1, 536/24.5, 707/102
• US Class Current: 702/19
• CPC Class Codes: C12Q 1/6811 Selection methods for production or design of target specific oligonucleotides or binding molecules
• 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
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids

Abstract

Where a DNA chip corresponding to a bacterium that is a subsequently added identification object is produced, temporal and pecuniary cost is reduced, and even where a probe unique to the DNA sequence of an identification object cannot be designed, precision in identifying DNA comprised in a sample is maximized. First, on designing a probe, a plurality of different probes are prepared to one kind of bacterium. Where some probes come to be not available by addition of bacteria that are new identification objects, identification is carried out using the remaining probes. Where a probe unique to an identification target bacterium cannot be designed, a probability of correct identification is increased by using multiple probes. Moreover, in consideration with a possibility that multiple kinds of bacteria simultaneously exist, a combination of probes that maximizes a probability of correct identification is selected.

Claims

1. A method of designing a biochip for identifying multiple kinds of targets via hybridization, comprising:

a step of reading data of base sequences of the targets;

for each of the targets, a step of (1) selecting one of partial sequences of a base sequence of a respective one of the targets, if said respective target has a partial sequence unique with respect to base sequences of other targets, or (2) selecting partial sequences of the base sequence of said respective one of the targets, as multiple probes, if said respective target does not have a partial sequence unique with respect to base sequences of other targets, each of said multiple probes having a low probability of mishybridization with said other targets;

a step of assigning an ID number to the biochip, and assigning said probe and said multiple probes to be spotted on predetermined positions on the biochip corresponding to said each of the targets respectively; and

a step of registering the ID number, said predetermined positions on the biochip, said probe and said multiple probes to be spotted on said predetermined positions on the biochip, and the corresponding targets in a memory.

2. The method according to claim 1, wherein the step of selecting multiple probes involves a step of selecting combinations of multiple probes corresponding to said respective target to increases the probability of specifically identifying the presence of said respective target, while avoiding any combination of probes corresponding to targets causing a mixed infection or a complication.

3. A computer program stored on a computer-readable recording medium for designing a biochip for identifying multiple kinds of targets via hybridization, comprising:

a module for reading data of base sequences of the targets;

a module, for each of the targets, for (1) selecting one of partial sequences of a base sequence of a respective one of the targets, if said respective target has a partial sequence unique with respect to base sequences of other targets, or (2) selecting partial sequences of the base sequence of said respective one of the targets, as multiple probes, if said respective target does not have a partial sequence unique with respect to base sequences of other targets, each of said multiple probes having a low probability of mishybridization with said other targets;

a module for assigning an ID number to the biochip, and assigning said probe and said multiple probes to be spotted on predetermined positions on the biochip corresponding to said each of the targets respectively; and

a module for registering the ID number, said predetermined positions on the biochip, said probe and said multiple probes to be spotted on said predetermined positions on the biochip, and the corresponding targets in a memory.

4. A computer-readable recording medium, which records a program for designing a biochip for identifying multiple kinds of targets via hybridization, comprising:

a module for reading data of base sequences of the targets;

a module, for each of the targets, for (1) selecting one of partial sequences of a base sequence of a respective one of the targets, if said respective target has a partial sequence unique with respect to base sequences of other targets, or (2) selecting partial sequences of the base sequence of said respective one of the targets, as multiple probes, if said respective target does not have a partial sequence unique with respect to base sequences of other targets, each of said multiple probes having a low probability of mishybridization with said other targets;

a module for assigning an ID number to the biochip, and assigning said probe and said multiple probes to be spotted on predetermined positions on the biochip corresponding to said each of the targets respectively; and

a module for registering the ID number, said predetermined positions on the biochip, said probe and said multiple probes to be spotted on said predetermined positions on the biochip, and the corresponding targets in a memory.